Running a business in Australia is rewarding, but let’s be honest managing payroll is one of the most stressful tasks for business owners. Between employee wages, superannuation, PAYG withholding, and reporting requirements, it’s easy to feel overwhelmed. Over the past 35 years as an accountant in Australia, I’ve seen businesses of all sizes from small cafes to growing trade companies struggle with payroll compliance.
The good news is that you don’t have to manage payroll alone. A registered BAS agent can step in and take care of payroll-related services, making your life much easier. But what exactly can a BAS agent do when it comes to payroll?
Let’s break it down.
First, What Is a BAS Agent?
A BAS agent is a professional registered with the Tax Practitioners Board (TPB). Their role is to provide services connected to the Business Activity Statement (BAS). While their primary work focuses on GST, PAYG withholding, and related taxes, payroll naturally overlaps with these areas.
Because payroll includes PAYG withholding and superannuation obligations, a registered BAS agent is authorised to manage many payroll functions.
Payroll Services a BAS Agent Can Provide
Here are the key payroll services BAS agents are legally allowed to provide:
1. Setting Up Payroll Systems
- A BAS agent can help you set up payroll correctly in accounting software like Xero, MYOB, or QuickBooks.
- They’ll ensure your payroll system is configured to calculate wages, PAYG withholding, and superannuation accurately.
- This avoids costly mistakes down the track.
2. Processing Employee Wages
- BAS agents can manage your regular pay runs.
- This includes calculating gross wages, deductions, overtime, and allowances.
- They’ll also ensure leave entitlements (sick leave, annual leave, long service leave) are tracked properly.
3. PAYG Withholding Management
- Employers are required to withhold tax (PAYG) from employee wages.
- A BAS agent can calculate and report PAYG withholding for each pay cycle.
- They also ensure that PAYG amounts are included correctly in your BAS lodgement.
4. Superannuation Guarantee (SG) Compliance
- Super is one of the most common areas where businesses fall behind.
- A BAS agent ensures you’re calculating and paying the correct super contributions (currently 11% of ordinary time earnings).
- They also help you use the ATO’s SuperStream system to lodge payments properly.
5. Single Touch Payroll (STP) Reporting
- Since STP became mandatory, employers must report wages, PAYG, and super data directly to the ATO with each pay run.
- A BAS agent can manage STP submissions for you, making sure your payroll data is always up to date with the ATO.
6. BAS Lodgement Related to Payroll
- Payroll and BAS are directly linked through PAYG withholding.
- A BAS agent calculates your PAYG obligations and reports them on your BAS.
- They can also liaise with the ATO if issues arise.
7. End-of-Year Payroll Finalisation
- At the end of the financial year, employers must finalise payroll records so employees can access income statements via myGov.
- A BAS agent can handle this process, ensuring all figures match ATO records.
8. Employee Onboarding Support
- BAS agents can guide you in setting up new employees correctly.
- This includes ensuring Tax File Number (TFN) declarations, super choice forms, and award-based pay rates are processed correctly.
9. Payroll Troubleshooting
- Payroll mistakes happen more often than you think.
- I’ve seen businesses overpay staff, underpay super, or miss PAYG deadlines.
- A BAS agent can identify and correct errors before they lead to penalties.
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Payroll Services BAS Agents Cannot Provide
While BAS agents cover a wide range of payroll services, there are some things they cannot do. For example:
- They cannot give income tax advice unless they are also registered tax agents.
- They cannot handle complex employee tax planning beyond payroll obligations.
- They may not act as HR consultants (e.g., resolving workplace disputes).
Always check the scope of your BAS agent’s registration.
Why Businesses Struggle With Payroll
Over my 35 years, I’ve seen a pattern of common payroll issues:
- Late super payments – Businesses think a few weeks won’t matter, but the ATO imposes harsh penalties.
- Incorrect PAYG withholding – Misclassifying workers (as contractors instead of employees) is a big risk.
- Award confusion – Australia’s award system is complicated, and underpayment cases are frequent.
- Poor record-keeping – Without proper software, it’s hard to track leave entitlements and overtime.
- Stress about ATO audits – Many business owners lose sleep worrying about whether they’re compliant.
The right BAS agent helps prevent these mistakes.
Benefits of Using a BAS Agent for Payroll
Hiring a BAS agent is not just about compliance it’s about peace of mind. Here’s what you gain:
- Accuracy – Payroll is done right the first time.
- Time Savings – Focus on running your business instead of processing wages.
- ATO Representation – Your BAS agent can liaise with the ATO if problems arise.
- Stress Reduction – No more worrying about missed deadlines or underpayments.
- Better Employee Trust – Staff are paid correctly and on time, improving workplace morale.
Real Cases From My Career
Let me share a few examples:
- A small construction firm in Adelaide kept forgetting super deadlines. When penalties hit, it cost thousands. After hiring a BAS agent, everything was automated and on time.
- A local café owner underpaid staff due to misinterpreting penalty rates. The BAS agent not only fixed the payroll but helped set up an award-compliant system.
- A marketing freelancer thought contractors didn’t need PAYG withholding. When the ATO disagreed, she faced back payments. A BAS agent helped her fix compliance and set up proper payroll.
How to Choose the Right BAS Agent for Payroll
When selecting a BAS agent, here’s what I recommend:
- Check TPB Registration – Only registered BAS agents can legally provide payroll-related BAS services.
- Ask About Payroll Experience – Make sure they’ve handled payroll in your industry.
- Look for Software Skills – Xero, MYOB, and QuickBooks expertise is essential.
- Confirm Insurance – They must have Professional Indemnity Insurance.
- See How They Communicate – A good BAS agent explains payroll clearly, without jargon.
Final Thoughts
Payroll isn’t just about paying staff it’s about complying with complex rules that link directly to BAS obligations. A registered BAS agent can handle payroll services like processing wages, PAYG withholding, superannuation, and STP reporting.
From my 35 years in practice, I can confidently say: businesses that use BAS agents for payroll sleep better at night. They know wages are accurate, super is paid, and the ATO won’t be knocking on their door with penalties.
So, if you’re feeling weighed down by payroll, don’t go it alone. A qualified BAS agent can take the load off your shoulders and let you focus on growing your business.
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