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Medicare, NDIS, and Tax: What Allied Health Practice Owners Often Get Wrong
Running an allied health practice is one of the most rewarding things you can do. You’re helping people, building a team, growing something meaningful. But the financial side of allied health is surprisingly complicated, and in my work with physiotherapy clinics, OT practices, speech pathology businesses, and psychology groups across Australia, the same three problems keep coming up.
Medicare billing confusion. Contractor classification headaches. NDIS GST mix-ups. None of these are obscure technical issues – they’re everyday situations that catch busy practice owners off guard, often at exactly the wrong moment.
Here’s what you need to know.
1. Medicare Billing: The Rules Changed in July 2025
If your practice bills Medicare for chronic disease management services, you need to be across the changes from 1 July 2025. The old Enhanced Primary Care (EPC) referral system has been replaced by GP Chronic Conditions Management Plan (GPCCMP) referrals. The core entitlement hasn’t changed – eligible patients still access up to five Medicare-subsidised allied health visits per calendar year – but the way referrals are structured and documented is different.
The most common billing mistakes I see are: billing a Medicare item before the prerequisite GP item has been claimed (allied health services don’t attract Medicare benefits until Services Australia has paid the GP item first); not tracking how many of a patient’s five annual visits have already been used across other providers; and billing individual item numbers for group sessions, when most chronic disease management items require face-to-face individual treatment of at least 20 minutes.
Medicare compliance checks are real. Providers can be required to submit evidence about the services they’ve billed, and discrepancies can result in repayment demands going back years. Make sure your practice management software reflects the GPCCMP changes, and have a process for confirming referral validity before each appointment.
2. Contractor vs Employee: This Is Where It Gets Expensive
Allied health practices commonly engage therapists on a contracting basis – sessional physios, locum OTs, contract speech pathologists. It’s a flexible model that suits a lot of practices. But the rules around who genuinely qualifies as a contractor have tightened considerably, and getting this wrong is one of the most expensive mistakes a practice can make.
Following High Court rulings in 2022 and the ATO’s updated Tax Ruling TR 2023/4, worker classification now focuses heavily on what the contract actually says rather than just how the working relationship looks day-to-day. And having a worker with an ABN doesn’t automatically make them a contractor for super or tax purposes.
There’s also a separate issue with superannuation that catches a lot of practices out. The Superannuation Guarantee legislation uses a broader definition of ‘employee’ than tax law does. A therapist who is technically a contractor for income tax purposes may still trigger super obligations if they provide mainly their own labour, can’t delegate the work, and are paid by time. With the super guarantee rate at 12% from 1 July 2025, the liability adds up quickly – and that’s before you factor in ATO penalties or potential payroll tax exposure from the Queensland Revenue Office.
If you’re not 100% confident about your current arrangements, a review is worth it. Sorting this out proactively is significantly cheaper than dealing with it during an audit.
3. NDIS and GST: Not as Straightforward as It Looks
Many allied health practices also provide services to NDIS participants, and this is where GST treatment gets messy. Most allied health services are GST-free when provided to NDIS participants under a registered plan – but not all NDIS-related services are automatically GST-free. It depends on whether the service is directly related to the participant’s disability support needs and how the funding is structured.
The common pitfalls: applying GST to services that should be GST-free (overcharging participants); treating all NDIS income as GST-free when some services – such as report writing or non-therapeutic consultations – may attract GST; and handling invoicing inconsistently when the same therapist sees both NDIS and non-NDIS clients in the same week.
The NDIS is also under increased compliance scrutiny. Auditors now expect digital record trails that link service delivery directly to billing. If your invoicing and record-keeping don’t align, that’s a risk worth addressing sooner rather than later.
The Bottom Line
None of these issues are insurmountable – most are straightforward to resolve once you know what you’re looking for. The challenge is that practice owners are flat-out delivering services, managing teams, and keeping clients happy. Keeping up with every ATO ruling on top of that is a big ask.
Getting your compliance right is the starting point – your tax, BAS, super obligations, and Medicare billing all need to be in order. But for a lot of allied health practices, that’s where the relationship with their accountant begins and ends. And honestly? There’s a lot more value on the table if you want it.
Depending on where your practice is at, that might look like cash flow planning to manage the peaks and troughs of a growing clinic, help structuring a new associate or contractor arrangement, working through a lease or equipment decision, or simply having someone to call when something changes and you’re not sure what it means for your business.
These aren’t services every practice needs all at once – but knowing that support is available when you do makes a real difference.
If any of the above sounds familiar – whether it’s getting your compliance foundations right or figuring out what comes next for your practice – I’d love to have a chat. No jargon, just plain English and practical next steps.
Ready to get your finances sorted?
Book a free 15-minute call with Amanda to talk through your practice’s specific situation. Whether you’re sorting out the compliance basics or looking for more hands-on support as your practice grows – we can create a custom package to suit you delivered with plain English answers and practical next steps.
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What It Actually Feels Like to Have an Accountant in Your Corner
When was the last time your accountant called you?
Not because something was due. Not because you had missed a deadline. Just to check in, see how things were going, and ask if there was anything on your mind.
If you are drawing a blank, you are not alone. For most business owners, the accountant relationship follows a predictable rhythm: radio silence for eleven months, followed by a frantic scramble at tax time. It works, technically. But it does not feel like much of a partnership.
At ASAP Solutions, we do things differently. And I want to share what that actually looks like from the client perspective – because until you have experienced year-round support, it is hard to imagine what you have been missing.
You stop carrying the mental load alone
Running a business means constantly juggling competing priorities. There is the work you actually do – seeing clients, managing projects, delivering services – and then there is everything else. The compliance deadlines. The payroll questions. The nagging feeling that you should probably be doing something about your tax situation but you are not quite sure what.
When you have an accountant who is genuinely in your corner, that mental load shifts. You are not the only one keeping track of what is due when. You are not lying awake wondering if you have set aside enough for your BAS. Someone else is paying attention – and they will give you a heads up before anything becomes urgent.
One of my clients described it as finally having a ‘financial spotter’. Like at the gym – you can push harder and take on more because someone has got your back if things get wobbly.
Questions get answered before they become problems
Here is something that happens regularly with our clients: they will mention something in passing during a check-in – maybe they are thinking about bringing on a contractor, or they have had an unusual expense, or they are wondering about a piece of equipment. And we can talk it through right then, while it is still in the ‘thinking about it’ stage.
Compare that to the alternative: you make a decision, implement it, and then find out months later at tax time that there was a better way to structure it. Or worse, that you have inadvertently created a compliance headache.
Proactive support means catching these things early. It means you can ask ‘quick question’ without feeling like you are bothering someone or watching the clock tick on billable hours. It means your accountant actually knows enough about your business to give you relevant advice, not generic guidance that may or may not apply to your situation.
Tax time becomes a non-event
I will be honest – when I tell people that our clients do not stress about tax time, they look at me like I have grown a second head. But it is true.
When you have been having regular conversations throughout the year, when your records are up to date because we have been working on them together, when you already know roughly what your tax position looks like because we have discussed it in your quarterly review – there is no drama. No surprises. No frantic gathering of receipts from the bottom of your bag.
End of financial year becomes just another month. You have already done the thinking, the planning, and the preparation. The actual lodgement is almost anticlimactic.
You actually understand your numbers
I believe that business owners deserve to understand their own finances. Not at a forensic accounting level – but enough to feel confident about where you stand and where you are heading.
When we work together throughout the year, there is time to explain things properly. To answer your questions without rushing. To help you see the patterns in your business and understand what the numbers are actually telling you. That is hard to do in a once-a-year meeting when we are both focused on getting your return lodged.
Our clients regularly tell me they feel more confident talking about money – with their bank, with potential investors, with business partners – because they actually know what is going on. They are not just nodding along and hoping for the best.
Tell us where you’re headed
Something I’ve learned over the years is that sometimes what your accountant thinks you need and what you’re actually wanting are two different things. Clarity on your vision for the future is so important to help you get their. If you’ve got something specific on your mind – a goal you’re working towards, a question you’ve been sitting on, a direction you want to take the business.
We want to know. Truly. Clear communication is the key to any good relationship, and ours is no different. The more you tell us about what you need and where you’re headed, the better we can help you get there.
Think of it like a sports team – we’re all working towards the same goal, but we need to understand your game plan to make the right plays. You set the strategy; we’ll help you execute it.
You have someone to celebrate the wins with
This one might sound a bit soft, but it matters. Running a business can be isolating. You hit a revenue milestone, you land a big client, you finally get your cash flow sorted – and there is no one who really gets why that is significant.
Your accountant sees the numbers. They know what you were working towards. When something good happens, they can appreciate it properly – because they understand the context and the effort it took to get there.
It sounds small, but having someone in your professional corner who notices your progress and acknowledges your wins? That is part of what makes the relationship feel like a partnership rather than a transaction.
Is this what you are looking for?
I started ASAP Solutions because I believed business owners deserved better than the traditional accounting experience. Not everyone wants or needs this kind of support – and that is completely fine. Some businesses genuinely only need an accountant once a year.
But if you have read this and thought ‘yes, that is what I have been missing’, then we should talk. Not a sales pitch – just a conversation to see if we would be a good fit for each other.
Because the right accountant relationship should not feel like a chore you put off as long as possible. It should feel like having someone genuinely in your corner.
Ready to experience the difference? Book a 15-minute chat with Amanda to see if ASAP Solutions is right for your business.
Getting Your Business Ready for the Holiday Break: Systems That Set You Up for Success
Christmas is coming!
And if you’re like most business owners, you’re already thinking about that glorious stretch of downtime (and maybe stressing a little about all the things to be done before that can happen).
But here’s the thing – taking a proper break shouldn’t mean crossing your fingers and hoping everything holds together while you’re away. Smart small business accounting practices mean setting up systems now so you can genuinely switch off later.
Let’s talk about putting the right systems in place so you can actually enjoy your break.
Why Systems Matter (Even for Small Breaks)
Whether closing for a week or taking the full summer shutdown, the businesses that I see bounce back strongest in January are the ones that planned ahead. Good small business accounting isn’t just about crunching numbers – it’s about creating systems that work even when you’re not there.
The Financial Housekeeping Checklist
Before you head off, get your financial admin sorted:
Cash flow planning – Map out what’s coming in and going out over the break period. Know when your bills are due and make sure you’ve got funds sitting in the right accounts. The last thing you want is a direct debit bouncing while you’re at the beach.
Invoicing ahead of time – Get December invoices out early. If you usually send them on the 20th, bring it forward. Your clients will be winding down too, and you want to catch them before their accounts payable person goes on leave.
Payment terms and reminders – Set up automated payment reminders for outstanding invoices. A gentle nudge before people disappear for the holidays can make a real difference to your January cash position.
Payroll sorted – If you’re paying staff early because of the break, communicate this clearly and get everything processed ahead of time.
Forward planning – Block out time in January before you leave. Book in your BAS preparation, time to catch up on admin work (invoicing and accounts reconciliation) and give yourself breathing room to ease back in.
What Good Planning Actually Looks Like
Here’s what you should aim for: You leave on your last day knowing everything’s handled. Your bills are paid or scheduled. Your clients know when you’ll be back. And you’ve got a realistic plan for ramping back up in January.
It’s not about having everything perfect – it’s about removing the uncertainty that stops you from properly switching off.
Quick Tip
NDIS and Allied Health
If you’re in these sectors, you’ve got some specific considerations:
Claiming deadlines – NDIS claims don’t stop for Christmas. Make sure your December claims are submitted before the break, and you’ve got a system for any that need to go in while you’re away.
Plan management – If you’re a plan manager, your participants still need access to funds. Make sure your systems can handle basic transactions even if you’re offline.
The Bottom Line
Taking a proper break isn’t about abandoning your business – it’s about setting it up so you can step away with confidence. The businesses that thrive long-term are the ones where owners know how to switch off and recharge.
Effective small business accounting means having systems that run smoothly whether you’re in the office or on holidays. If you want someone to help you set up your accounts system to become more automated, get on top of your accounts or see how you can streamline your business for next year; that’s exactly the kind of planning conversation we can have. Book in a chat and let’s take the headache out of your accounts for next year!