Reconciling Medicare, Private, NDIS and EAP Payments: A Practical Guide for Psychology Practices
By Bookkeeping Central · Published · 7 min read
You glance at the bank feed and see three deposits that don't obviously match anything in your appointment book. One might be Medicare. One's probably a health fund. The third could be an EAP invoice that was overdue three weeks ago.
If your practice bills more than one payer, this can become a regular reconciliation problem, not because anything's gone wrong, but because Medicare, private health, NDIS and EAP payments each move through their own system, on their own timeline, with their own kind of paperwork.
Start by Sorting, Not Matching
The biggest time-waster in reconciliation is comparing a bank total to your total billings for the week. It won't line up, because each payment stream moves through its own report and its own timing.
Avoid it: Before you match anything, sort your deposits by payer first. Pull the Medicare payment report, the HICAPS settlement, the EAP remittance and the relevant NDIS payment report separately, and work through them one at a time.
Reconciling Medicare Payments
The detail that trips practices up most is the claiming method, not the fee. A bulk-billed session gets paid to the practice by Medicare directly.
With a patient claim, the client will commonly pay the practice in full and receive the Medicare benefit themselves. Unpaid accounts follow a different process, so the practice should record how each claim was submitted and who is expected to receive the benefit. Services Australia confirms that bulk-billed benefits are assigned to the provider, while paid and unpaid patient claims can follow different payment processes.
Both bulk-billed and patient-claim sessions are valid revenue. But log a session simply as "Medicare" without noting which method applied, and it can sit in your books looking like an outstanding Medicare payment that was never actually coming to you.
Avoid it: Record the claiming method at the time of the appointment, not later. Use the Medicare bulk bill payment report, or the Easyclaim report if you're claiming through a terminal, as your reference for matching, not the bank feed on its own.
Reconciling Private Health and HICAPS
Private health rebates for psychology can vary by fund, policy, service and provider eligibility, so there's no single rebate schedule that applies to every client. Two clients on the same fund can receive different benefits depending on their specific policy, which is why each claim needs to be matched against its own records.
Record the health-fund benefit and the patient’s contribution against the same invoice. Match the receipts using the relevant claim, remittance and payment records, rather than assuming one bank deposit will equal the full appointment fee.
Avoid it: Use the claim, remittance and payment records to confirm that the health-fund benefit and the patient's contribution have both been allocated to the correct invoice. Where there's no HICAPS terminal involved, record the client's full payment against the invoice and retain the relevant payment record; the client handles their separate claim with the fund.
Reconciling EAP Payments
EAP work is genuinely different again. The client isn't the one paying, the employer or EAP provider is, and you're invoicing that organisation directly rather than billing at the point of service.
Every EAP arrangement is its own contract, so invoicing frequency, payment terms and how much detail comes through on the remittance all vary by provider. Some pay against a single invoice per client. Others send one payment covering several sessions or several employees under one combined reference, which is precisely what makes an EAP remittance hard to reconcile on sight.
Avoid it: Don't expect an EAP remittance to break down session by session. Match it back to the specific invoice or invoices it relates to, and keep the invoice itself as your record of what was actually claimed.
Not sure your reconciliation process is catching everything? Get a free financial health check and we'll look at how your practice currently matches payments to claims. See Pricing | 1300 855 763
Where NDIS Fits Here
NDIS payments follow their own logic again, and which one applies determines where you even start looking for the money. For NDIA-managed funding, you submit payment requests through the relevant provider system. For plan-managed funding, you invoice the plan manager. For self-managed funding, the participant or their representative pays your invoice (NDIS guide to getting paid).
Reconcile the payment against the relevant portal report, plan-manager remittance or participant invoice, not the bank feed alone. NDIS reconciliation deserves its own detailed guide, and we've written one: why your NDIS payment may not match the claims you submitted. The key thing to take from this section is simply to identify how the participant's funding is managed before you go looking for the payment.
A Simple Reconciliation Checklist
Run through this each time you sit down to reconcile, not just when something looks wrong:
- Sort deposits by payment source before comparing anything to your billing records
- Confirm bulk-billed vs. patient-claim status, and who the benefit was assigned to, for every Medicare session
- Record the health-fund benefit and the patient's contribution against the same invoice, then match both using the relevant claim, remittance and payment records
- Match EAP remittances to specific invoices, not to a running total
- Confirm how each NDIS participant's funding is managed, and check the relevant portal report, plan-manager remittance or participant invoice
- Keep a short list of anything unresolved and revisit it weekly, not monthly
What to Check When Something Doesn't Match
Common causes of payment mismatches include:
- Wrong stream coding. A session logged as Medicare when it was actually private health or EAP-funded.
- Timing. The service, the claim and the payment landing in different reporting periods.
- An adjusted or rejected claim. Only visible in the payer's own report, not the bank feed.
- Separate gap and benefit records. With private health, the client's contribution and the fund's benefit still need to be allocated against the same invoice.
Working through this list is usually faster than assuming a mismatch is a mistake.
Keep the Right Paperwork
Alongside your usual invoices and bank records, hold on to the Medicare or Easyclaim report, the HICAPS settlement record, the specific EAP invoice for each payment and the relevant NDIS portal report, plan-manager remittance or participant invoice. A simple exceptions log, noting the date, the client, the payment stream and what you expected versus what arrived, saves a lot of time chasing the same query twice.
Reconciliation Shouldn't Be the Hard Part
Running a multi-payer practice already takes enough of your attention. Reconciliation is meant to confirm what's coming in, not become a project in its own right. If you want the bigger picture on managing income across Medicare, NDIS and private billing more broadly, our article on managing multiple revenue streams covers that ground. You can also see how we support psychology practices with ongoing bookkeeping.
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