Overcoming Payroll Compliance & Integration Challenges: Essential Strategies for Australian Executives & Business Owners

Debbie C.
Jan 11
4 min read

Updated: Jan 12

As a business owner or executive in Australia, you're no stranger to the complexities and heart-breaking pressure of managing payroll for all of your employees. With regulations evolving so often —most notably, the introduction of Payday Super from 1 July 2026¹, requiring employers to pay superannuation contributions at the same time as salary and wages² —and the ongoing need for seamless system integrations, it's easy to feel overwhelmed, you are not alone. These challenges don't have to derail your operations, RUNPAY is here to help guide you to reliable solutions and business resources. In this post, we'll outline the key issues facing executives, business owners, and their payroll leads, drawing on official resources and real-world industry insights. We'll also provide practical actions to help reduce your business risk, so you can communicate these strategies clearly to your team. If you're exploring payroll solutions, our earlier guide titled 'Popular Payroll Solutions in Australia: A Beginner's Guide' provides an introductory foundation to assist you.³

The Evolving Landscape of Payroll Compliance in 2026

Australian payroll compliance is set for one of its most significant shifts in decades, with Payday Super commencing on 1 July 2026.¹⁴ This reform requires employers to pay superannuation guarantee (SG) contributions on payday, with funds reaching employees' super funds within 7 business days.² The legislation, which received Royal Assent in November 2025, aims to reduce unpaid and underpaid super while aligning payments with regular wage cycles.⁵ Additional pressures include ongoing changes to the Fair Work Act, Modern Awards, and National Employment Standards (NES), as well as the need to maintain accurate Single Touch Payroll (STP) reporting.⁶ Without proactive preparation, risks such as ATO penalties, underpayments, or audit exposure can escalate quite quickly and very often unfortunately unexpectedly and unbeknownst to a business owner, especially when it comes to Payroll, your people and Employment Law.⁷

Common Integration Hurdles and Their Impacts

Linking Payroll (with HR, Finance) Plus Business Development (Sales and Marketing), time-tracking for staff including project-management or other tools often creates silos and inefficiencies across business operations. Poor integration across a business, remains a huge pain point for all payroll teams, leading to business administrative expense from manual data entry errors, incorrect leave balances, and compliance breaches.⁸ In Australia's increasingly complex payroll environment, integrating with platforms like Xero is essential but challenging. Setup issues —such as data mismatches —can waste hours upon hours on fixes and heighten the risk of non-compliance.⁹ For business owners and executives, this means higher operational costs, frustrated teams, and potential legal or reputational damage.¹⁰ We've explored similar efficiency opportunities in our post titled 'Maximise Business Efficiency with Australia's Best Payroll Systems', where automated integrations were highlighted as transformative.¹¹

Key Challenges Faced by Executives and Payroll Teams

Executives and payroll leads commonly face these hurdles:

Keeping Up with Legislation — Changes like Payday Super's real-time STP reporting requirements and Award interpretations demand constant vigilance.¹²
Cash Flow and Operational Strain — More frequent super payments under Payday Super may impact cash flow, necessitating updated processes.¹³
Integration Compatibility — Technical mismatches can lead to errors and penalties.¹⁴
Data Accuracy and Security — Manual processes increase error risks, while weak integrations raise data breach vulnerabilities.

These issues drain resources and expose your business to unnecessary risk.

Actionable Strategies to Mitigate Risks

Here are some straightforward steps to reduce your business risk and empower your teams to feel intimately connected to your business purpose too:

Audit and Integrate Systems Early
Perform a thorough data audit before linking your systems to prevent gaps or duplicates.¹⁵ Choose platforms that integrate seamlessly with accounting software for real-time accuracy.¹⁶
Prepare for Payday Super
Review and update your payroll software by mid-2026 to automate super payments and align with STP.¹⁷ This will position you for compliance and audit-readiness, with the ATO advising that they will take a more lenient approach in the first year (1 July 2026 to 30 June 2027) for employers who make honest and genuine efforts to meet the cut-off date.¹⁸
Invest in Automation and Training
Adopt systems (or solutions like Payroll StandardⓇ) with built-in compliance alerts.¹⁹ Also take some time to just speak with your Payroll leads to discover if there is need or business training on new features to minimise errors and boost efficiency with actions.²⁰ Your payoll team are your best resource when it comes to a cycle of getting tasks done on time - just ask them for structured feedback on progress not problems.
Stay Informed with Resources
Track key dates using our RUNPAY Master Calendar. For more insights, see our post titled 'The Future of Payroll: Embracing Change for 2026 and Beyond.'²¹
Partner with an Expert
If managing integrations and compliance in-house feels too overwhelming, consider outsourced solutions to lower your risk exposure.²²

Implementing these steps not only ensures compliance (and demonstrates your attempt to do so) but also enhances efficiency and employee trust.

Final Thoughts By RUNPAY™️

Navigating payroll compliance and integrations in 2026 doesn't need to be a headache. By tackling these challenges proactively with practical strategies, you can protect your business and support your teams effectively. Are you ready for 2026? Discover how RUNPAY™️ can transform your approach, just read this article: 'How RUNPAY™ Revolutionises Payroll Procurement in Australia'.

References