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Medicare patient claims: who gets the rebate

A Medicare patient claim is settled by the patient at the desk, and Services Australia pays the rebate into the patient's own registered account. Where the invoice was paid before lodgement, no Medicare deposit is due, so nothing should sit waiting for one. Post the full fee to the Medicare clinical revenue account against the payment the patient made, and keep the clearing account for bulk bill.

Key facts

Who pays the practice
The patient, at the appointment, before the claim can be lodged1
Who gets the rebate
The patient, into the bank account they registered with Medicare5
Time to the rebate
One to three business days, to the patient rather than to the practice5
Deposit shape
The patient's own card payment or transfer, one payment per invoice5
Breakdown file
None on the practice side, because the rebate is not practice money1
Rejections
A rejected claim leaves the practice whole, since the fee was collected before lodgement1
The gap only exception
Lodging an unpaid invoice sends a cheque in the provider's name to the patient's address3
Who the 90 day scheme covers
Allied health professionals, optometrists and dentists are not eligible to participate, so an unbanked cheque does not convert to an electronic transfer for an allied health practice13
Why a gap means a patient claim
A gap cannot be charged on a bulk billed service, which has to be claimed for its whole value2
GST treatment
A Medicare benefit is payable for the claimed service, which makes it GST free as a medical service9
Revenue account in the allied health template
401 Clinical services, Medicare, at the GST free income rate, which the template's own note says carries patient claim invoices as well as bulk billed ones8

One claiming screen, three endings

A Medicare patient claim looks like a bulk bill claim on the claiming screen and behaves quite differently in the books. The practice charges the patient, lodges the claim on the patient's behalf, and Services Australia pays the benefit to whoever the claim names as the claimant. Where that money ends up turns on one thing: whether the invoice was settled before the claim went out.

  • The invoice is paid in full and the patient is the claimant. Medicare pays the rebate into the patient's own registered account, and the practice has already been paid.
  • The invoice is paid in full and someone else is nominated as the claimant. Cliniko's claiming screen offers that choice, and the rebate follows the nomination rather than the patient.
  • The invoice is lodged unpaid or part paid. No client bank details travel with the claim, so Medicare issues a cheque in the provider's name and posts it to the patient. This is the path a gap only claim takes.

Only the third ending leaves anything outstanding in the practice's books, and it is the ending the claiming documentation stops short of.

Where the rebate actually goes

Zanda's help centre puts it plainly: Medicare pays the rebate directly into the bank account the client has registered with Medicare, typically within one to three business days. The practice system does not track that payout, because it is not the practice's money to track.

So on a claim lodged against a paid invoice, the whole of the practice's revenue arrives from the patient, at the desk, on the day of the appointment. Cliniko sets that as its own rule: payment has to be taken from the patient before Cliniko will process the patient claim. Other systems will lodge an unpaid or part paid account, and that is the path the cheque comes back on.

Medicare patient claim, appointment to rebateMoney moves from the patient to the practice bank account in one payment on the day of the appointment, the claim goes to Services Australia and comes back assessed, the rebate travels on to the patient's own registered account rather than to the practice, and a side leg holds the card processing fee outside the claimed amount.Medicare patient claim, appointment torebateDay of servicePatient paysThe patient settles the invoice in fullat the appointment, by card or bytransfer.Once the invoice is paidClaim lodgedThe practice lodges the claim on thepatient's behalf through its MedicareOnline channel.Within a few secondsClaim assessedServices Australia answers the practicesystem with the claim assessed, pendedor rejected.One to three business daysRebate to the patientThe benefit is paid into the bankaccount the patient registered withMedicare.Card processing feeThe surcharge the practice adds isexcluded from the claimed amount andstays on the invoice as its own line.Lands inThe practice bank account, as thepatient's own payment
Plate 1The patient claim money flow, with the rebate leg ending somewhere the practice ledger cannot see.

No Medicare deposit on a paid claim

The reconciliation error this page exists to prevent is treating a patient claim the way a bulk bill run is treated. A Medicare bulk bill claim is assigned to the practice and paid to the practice, which is why it earns a clearing account that holds approved claims until the payment run lands. A patient claim earns nothing of the kind. Put one through the clearing account and the balance sits there with nothing coming to clear it.

Booked as though Medicare would pay beside Booked as a patient claimTwo ledger columns for the same appointment, one booked as though Medicare would pay the practice and one booked against the patient's own payment, across four rows: Medicare clearing, accounts receivable, clinical services for Medicare, and the bank.Booked asthoughMedicarewould payBooked as apatient claimMedicareclearingHolds therebate portionas though adeposit wereon its wayNo entry,because noMedicaredeposit isdueAccountsreceivableInvoice leftopen, waitingon a MedicarepaymentClosed onthe day thepatient paidClinicalservices,MedicareRecognised atthe schedulebenefit onlyRecognisedat the fullfee thepatient waschargedBankPatientpaymentsittingunmatchedagainst aMedicareexpectationPatientpaymentmatched tothe invoiceit settled
Plate 2The same appointment booked two ways, and the clearing balance that has nothing coming to clear it.

The tell is a Medicare clearing balance that grows by the rebate portion of every privately billed appointment and gets written back at month end for a reason nobody can name. The fix sits upstream of the bank feed. The invoice was closed by the patient's payment on the day it was made, and the practice's revenue is the full fee rather than the schedule benefit.

The cheque that sits with the patient

Pay doctor via claimant is the gap only version of a patient claim, and it is why a Medicare receivable can stay open for months. Best Practice's knowledge base sets out the mechanics: the cheque is issued in the provider's name and sent to the patient's last known address as recorded by Medicare, and those cheques cannot be sent to providers or to a patient at a provider's address. There is a scheme that cancels an unbanked cheque after 90 days and pays the practitioner the Medicare schedule fee by electronic transfer, and Services Australia names allied health professionals, optometrists and dentists as ineligible for it. For those practices the money comes through the cheque itself.

Most patients just put the cheques in the bin and the doctor waits the 90 days for Medicare to send the rebate, but we have seen situations where some patients successfully bank those cheques into their own bank accounts and that is quite a big problem.6

That report is written about doctors, who do have the 90 day fallback, and the majority of the practitioners using the scheme were believed to be GPs. Across the 2017 to 2018 financial year it puts scheme expenditure at 322 million dollars, covering 1.2 million patients and 3.2 million services provided by more than 39,000 practitioners, and separately puts the mailing at more than 1.2 million paper cheques totalling 320 million dollars. The scale matters more than the figure. An allied health practice billing gap only is carrying a receivable that a patient's kitchen drawer controls, with no fallback behind it.

The card fee that sits outside the claim

One step in the claiming screen changes what the ledger holds. Where the practice adds a card processing fee to the invoice, that item has to be switched off before the claim goes out so it is not included in the claimed amount. Zanda's instruction is to disable the active toggle on the Stripe processing fee service item.

  1. The claim carries the clinical service alone, so the rebate the patient receives is based on the service rather than on the surcharge.
  2. The invoice the practice raises still carries both lines, because the patient paid both.
  3. The surcharge sits on its own invoice line and its own account, so the claimed amount and the fee income stay apart in the ledger.
  4. A claim lodged with the fee attached states a service amount the practice did not charge for the service, which is worth correcting before it becomes a pattern.

The GST treatment

The payer does not decide the treatment. The ATO puts the recipient of the supply at whoever engages the practitioner to provide the service, which on a patient claim is the person treated, so the service itself decides it. A service a Medicare benefit is payable for is a medical service, and medical services are GST free, which covers the appointment the claim was lodged against. Where no Medicare benefit is payable, s38-10 does the work instead: the supply is GST free where it is a listed health service, performed by a recognised health professional in that listed service, and generally accepted in that profession as necessary for the appropriate treatment of the recipient of the supply.

Medicare bulk billThe treatment card for Medicare funded revenue, showing the allied health and psychology templates posting it to account 401, Clinical services, Medicare, at the GST free income rate, and the NDIS provider template falling through to its practice default account 400 at the same rate.Medicare bulk billEvery service category with no row of itsownallied-health-by-funding-source401 Clinical services, MedicareGST Free IncomeResolved by the funding source default row.See account 401.ndis-provider-plan-managed400 Clinical services, private patientsGST Free IncomeResolved by the practice default row.The required safety net when funding_sourceitself has not resolved. Should almost neverfire; a line landing here belongs in thequestions queue (docs/02-product-spec.md,section 6.1).psychology-with-booking-deposits401 Clinical services, MedicareGST Free IncomeResolved by the funding source default row.See account 401.The canonical templates do not post this thesame way, so each template is shown as itposts it.This is the default posting for the fundingsource, so any category with a row of itsown overrides it.In allied-health-by-funding-source nocategory overrides it.In ndis-provider-plan-managed no categoryoverrides it.In psychology-with-booking-deposits nocategory overrides it.
Plate 3The Medicare posting, read from the canonical templates rather than typed onto this page.

In the canonical allied health template that is account 401, Clinical services, Medicare, at the GST free income rate, and the psychology template posts it the same way. That account carries patient claim invoices alongside bulk billed ones, because the revenue treatment is the same either way and only the settlement rail differs. The NDIS provider template spells out no Medicare row, so a Medicare line there falls through to its practice default account and belongs in the questions queue rather than posted silently. That same template gives a report written for a third party, a supervision session and a product the patient takes home a row each at the taxable rate, which is why the standing map holds a row per service category instead of one row per funder. The ATO's own examples run the same way: a report written for an insurer is not GST free where no Medicare benefit is payable for it and it is not a natural part of the treatment, and the extra dressings a patient takes home after a consultation are not GST free even though the consultation was.

The Xero pattern for a patient claim

The pattern here is the private billing pattern, and its whole virtue is what it leaves out.

  1. The invoice is raised for the full fee the patient was charged, with any surcharge as its own line.
  2. The payment is receipted on the day the patient paid, through whichever rail the practice takes money on.
  3. The bank line for that rail is matched to the payment, and no clearing account is involved.
  4. Where the claim went out unpaid, the rebate portion stays open against Medicare until the cheque is banked or the transfer arrives, and that is the one balance worth ageing.

Surgical Partners tells practices reconciling Medicare in Xero to lean on the automatic match when the amount and the reference agree, and on find and match when the amount agrees and the reference does not. That guidance is written for bulk bill deposits. On a patient claim there is nothing from Medicare in the bank feed to match, and holding both facts at once is what a mixed billing practice has to do twice a day.

What Ledger Map does with it

Ledger Map keeps one approved map per practice and reads every line through it. A privately billed appointment resolves to its own account and tax rate, the patient's payment posts as one balanced document set, and the bank feed is left holding a single exact match for a person to accept. Where a gap only claim is involved, the rebate portion is raised as a question with the options laid out, because the invoice on its own cannot say whether a cheque has changed hands.

None of the treatments above was chosen by the product. Each is read from the canonical template the practice picked at setup, and the practice signs off the map before an invoice syncs. How it works walks through that map and the approval step in front of it.

Questions

  • Why has no Medicare deposit arrived for a patient claim?

    Because the rebate was paid to the patient. On a patient claim the practice collects the full fee at the appointment and Services Australia pays the benefit into the account the patient registered with Medicare. Where the claim went out against a paid invoice, no practice deposit is due, so an invoice left open against Medicare, or a clearing balance carrying the rebate portion, is the entry to correct rather than the payment to chase. A claim lodged unpaid is the one exception, and it pays by cheque to the patient first.

  • What is the difference between a patient claim and bulk billing?

    Who gets paid. Bulk billing assigns the benefit to the practice, so Medicare pays the practice and no gap can be charged, since the claim has to go in for the whole value of the service. A patient claim leaves the patient paying the practice, and the rebate goes back to the patient. Taking any payment from the patient means the claim is a patient claim.

  • How long does a Medicare patient claim rebate take?

    Typically one to three business days into the patient's registered bank account, on a practice management vendor's figure rather than a published Services Australia standard. The practice's own money does not wait on it, so the only timing that touches the ledger is the date the patient paid.

  • Why did Medicare send a cheque in the practice's name to the patient?

    Because the claim went out with the invoice unpaid or part paid, so no client bank details travelled with it. That is the pay doctor via claimant path: the cheque is made out to the provider and posted to the patient's last known address. The 90 day scheme that cancels an unbanked cheque and pays the practitioner by electronic transfer names allied health professionals, optometrists and dentists as ineligible, so an allied health practice waits on the cheque itself.

  • Should a card surcharge be included in a Medicare patient claim?

    No. Zanda's guidance is to switch the processing fee item off before lodging, so the claim carries the clinical service alone. The invoice still shows both lines, because the patient paid both, and the surcharge sits on its own line and its own account so the claimed amount matches the fee for the service.

  • Is a patient claim consultation GST free?

    It turns on the service, not on who paid. A service a Medicare benefit is payable for is a medical service, which the ATO treats as GST free, and the canonical templates post the revenue as GST free income. Where no Medicare benefit is payable, the supply is GST free only where it is a listed health service performed by a recognised health professional in that listed service and generally accepted in that profession as necessary for the appropriate treatment of the recipient of the supply, which is the s38-10 test. A report written for a third party and a product the patient takes home sit outside both, and the allied health template gives each a taxable row.

Sources

Open questions

  • The Services Australia page for the pay doctor cheque scheme refuses an automated fetch, so it is read here from an Internet Archive capture of the page as last updated 3 March 2022. Whether the eligibility list has moved since then was not confirmed against the live page.
  • The one to three business day rebate window is a practice management vendor's figure rather than a published Services Australia service standard, so treat it as typical.
  • The cheque volume and value quoted on this page are the 2017 to 2018 financial year figures reported in 2019. No later count could be found, so they describe the scale of the scheme at that time rather than the position today.
  • How a card processing surcharge on a GST free consultation is treated for GST is not settled by any source read for this page, and the canonical templates carry no surcharge revenue row, so the page says only that the surcharge sits outside the claimed amount and on its own account.
  • Whether nominating a claimant other than the patient changes anything in the practice's books is not addressed by any source read for this page.
  • The answer landscape for this page was reconstructed through a real time search delegate after the search budget ran out, and google.com.au blocked a direct fetch, so the ranking in the brief is reconstructed and no claim is made about People Also Ask or an AI Overview.
  1. Process patient claims for Medicare

    Cliniko. Retrieved 29 Aug 2026.

    primary

  2. Cliniko Medicare frequently asked questions

    Cliniko. Retrieved 29 Aug 2026.

    secondary

  3. Medicare and DVA gap payments

    Best Practice Software. Retrieved 29 Aug 2026.

    secondary

  4. GST and health

    Australian Taxation Office. Retrieved 29 Aug 2026. Source updated 13 Jun 2024.

    primary

  5. Submitting a patient claim, Australia only

    Zanda. Retrieved 2 Sep 2026.

    primary

  6. Medicare asking one million patients to hand deliver cheques to pay doctors

    Synapse Medical Services. Retrieved 2 Sep 2026. Source updated 4 Jul 2019.

    secondary

  7. How to reconcile Medicare payments

    Surgical Partners. Retrieved 2 Sep 2026.

    secondary

  8. Allied health by funding source, the canonical template

    Ledger Map. Retrieved 2 Sep 2026.

    primary

  9. Medical services, GST and health

    Australian Taxation Office. Retrieved 3 Sep 2026. Source updated 12 Jun 2024.

    primary

  10. Recipient of the supply, GST and health

    Australian Taxation Office. Retrieved 3 Sep 2026. Source updated 12 Jun 2024.

    primary

  11. Other health services, GST and health

    Australian Taxation Office. Retrieved 3 Sep 2026. Source updated 12 Jun 2024.

    primary

  12. Goods supplied as part of a GST free health service, GST and health

    Australian Taxation Office. Retrieved 3 Sep 2026. Source updated 12 Jun 2024.

    primary

  13. The 90 day pay doctor cheque scheme, archived capture of the page as last updated 3 March 2022

    Services Australia. Retrieved 4 Sep 2026. Source updated 3 Mar 2022.

    primary

Review

Last reviewed 4 Sep 2026 by Shane

General information for Australian allied health practices, not tax advice. Confirm a treatment with your BAS agent or accountant before you post it.

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