Australian Payroll Reports and Compliance 2026. Payroll isn’t just paying people; it’s a data pipeline that hits tax, super, audits, and trust. Reports are how you prove that what you paid matches what you told government, that super is accruing and landing, and that managers aren’t making up the rules one exception at a time. If you build the right reporting spine, quarter-end becomes a tick-box, not a fire drill.
Your reporting spine (the absolute minimum)
There are two mirrors you should look into every pay cycle:
- The STP mirror: a preview of your Single Touch Payroll Phase 2 event that shows disaggregated earnings, ordinary time, paid leave, allowances by type, overtime, bonuses/commissions, directors’ fees, and salary sacrifice, exactly as the ATO expects to see them. If your preview doesn’t match your draft payslips line-for-line, fix the mapping now.
- The BAS mirror (W1/W2): an internal view that totals payments subject to withholding (W1) and the amount withheld (W2). The ATO’s BAS uses these labels; build your report to mirror them so prefill doesn’t surprise you.
Run both mirrors every pay. You’ll stop most problems before they harden into quarter-end noise.
The core reports (what they show and how to use them)
1) Pay-run summary (by employee and in total)
This is your “what did we just do?” snapshot, gross by component, PAYG withheld, deductions, net pay, and employer on-costs. Treat it as your sign-off pack alongside the STP preview so leadership signs what will be sent to the ATO, not a different version in spreadsheets. Tie the component lines to your STP categories so names match on screen and in the file.
2) Payroll register / year-to-date (YTD) by employee
Shows each worker’s cumulative earnings components and tax to date. Use it to investigate any “myGov doesn’t match my payslip” questions, because STP sends disaggregated components now, if a piece is mis-mapped, you’ll see it here first.
3) W1/W2 reconciliation view
A purpose-built report that rolls up only payments subject to withholding to W1 and the withheld tax to W2. If this view doesn’t equal the BAS draft (or ATO prefill fed from STP), you have a mapping issue, fix the pay items, don’t fudge the BAS.
4) STP pay-event preview (Phase 2)
Your final check before lodging: all the disaggregated lines, income types, and allowance purposes the ATO demands in Phase 2. It’s the fastest way to catch buried “all-purpose” allowances or mis-labelled items that would make STP disagree with payslips. Lodge only after this matches the pay-run summary.
5) Allowances detail (by type, by employee)
A cut that shows which allowances you paid (travel, car, overtime meal, tool, laundry, first-aid, etc.) and how they’re mapped in STP. It keeps your disaggregation honest and helps managers see what policies are driving spend.
6) Superannuation: accrued vs paid (by employee and by fund)
You want two angles: accruals at 12% of OTE in the period, and payments out to funds. Differences should be timing only. This is the early-warning system that stops the Super Guarantee Charge (SGC) conversation before it starts; OTE settings come from SGR 2009/2, so document them and line them up with this report.
7) Super payable ageing
Lists unpaid super by fund and period. If anything is drifting beyond the contribution due date, you’re courting SGC. Use this to schedule earlier contributions (monthly or per-pay) so “payday super” in 2026 isn’t a shock to cashflow. (Even before the change, ageing keeps you honest.)
8) Super clearing reconciliation
Ties your payroll’s “paid to fund” lines to clearing-house batch confirmations and bank amounts. You’ll use it any time an employee asks “has my super landed?” or a fund queries a missing contribution.
9) Deductions ledger
Salary sacrifice to super (pre-tax), union fees, novated leases, overpayment recoveries, each deduction needs a clean trail. Your ledger should show amount, destination account/fund, and YTD. That protects W1/W2 maths and gives Finance the audit evidence it needs.
10) Leave liability and balances
Two views: entitlements (what employees have available) and liability $ (your provision). You’ll use balances for roster planning and liability for month-end. Not legally required on payslips, but you must provide balances on request; still, reporting them proactively reduces noise.
11) Overtime and penalty hours by team
A simple operational report that correlates with fatigue, errors, and cost blowouts. Where you see overtime up and annual-leave uptake down, you’ve found a psychosocial-risk hotspot and a margin problem in one spot. (Fix the work design, not just the roster.)
12) Employee masterfile change log
Who changed a tax file number, rate, bank account, super fund, or address, and when? That’s your internal control against fraud and the fastest way to investigate “mystery” variances.
13) Payroll-tax wages by state/territory
If you’re near thresholds, you need a clean split of taxable wages by jurisdiction with the local add-ins your revenue office cares about. This report saves you from month-end scrambles and year-end reconciliations that chew days.
14) RFBA (reportable fringe benefits amounts) and FBT alignment
An annual view that links your FBT working papers (FBT year 1 Apr–31 Mar) to the RFBA figures you’ll include when you finalise STP at year-end. It stops the “March vs June” calendar confusion.
15) End-of-year STP finalisation status
Shows which employees are finalised and which are pending so you don’t miss the 14 July employer deadline (different dates may apply for closely-held payees). This is how you avoid the July inbox full of “my income statement isn’t tax-ready.”
How to run the cadence (so nothing slips)
Every pay run
Close timesheets, run the pay-run summary, STP Phase-2 preview, and W1/W2 view. Check that allowance names on payslips equal allowance types in the STP preview. If they diverge, you have a mapping problem. Lodge STP on or before payday.
Within 48 hours after payday
Confirm the ABA or bank batch equals the net-pay total; check a sample of employee YTD against the STP view; file the signed approval pack. If your software supports it, attach the reports to the pay-run record.
Monthly
Run Super accrued vs paid and Super payable ageing; pay contributions early and reconcile to clearing confirmations. Refresh the deductions ledger and fix any mis-coded salary sacrifice before BAS month.
Quarterly
Use the W1/W2 view to prepare your BAS and compare to ATO prefill (which draws from STP). If it doesn’t match, hunt the mapping error, not the calculator. For larger groups, roll up the payroll-tax wages by state.
End of financial year (June/July)
Close out any back-payments, check RFBA amounts, and make your STP finalisation declaration by 14 July (unless you qualify for the closely-held timetable). Tell employees if you’re delaying finalisation and why; they’re watching myGov.
Labels that must agree everywhere
One of the easiest ways to cut noise is to make names travel. If the payslip says “Travel allowance”, the STP line should say Travel allowance (Phase-2 allowance type), and the W1/W2 view should count it correctly at W1. Same idea for salary sacrifice, paid leave, and overtime. Disaggregation demands consistency; don’t let “creative” item names creep in.
Super: report to the ruling, not to vibes
Your super reports must line up with SGR 2009/2 (what is and isn’t ordinary time earnings). Document your treatment of each allowance type once (expense-style travel/tool often not OTE; “all-purpose” linked to ordinary hours often is), encode it in pay items, and make sure accrued vs paid reflects that logic. Auditors look for the paper trail; give them one.
Common reporting traps (and how to avoid them)
Burying allowances in base pay
Phase 2 won’t forgive it. Split “all-purpose” allowances into their real components and tag them, or your STP will misstate gross and your BAS prefill won’t tie out.
Treating reimbursements like income
A reimbursement isn’t wages; it shouldn’t inflate W1 or appear as earnings in STP. Keep reimbursements in AP with receipts and, if you move cash via payroll for speed, configure the item out of STP and W1/W2. (You’ll thank yourself at BAS time.)
Super reports that ignore timing
“Accrued” without “paid” is how you drift into SGC. Age it monthly and clear it before the deadline; you want timing differences only, never omissions.
EOFY left to July panic
Finalisation needs clean YTDs. If your YTD register doesn’t match what the ATO sees, fix mapping and re-lodge events before 30 June where possible. Aim to finalise by 14 July so employees see “Tax ready” on time.
Build this once and stop reinventing it
Standard names in the software
Name pay items like a human and bake the downstream treatment into the description: “Travel allowance | STP: travel | W1: yes | OTE: no.” Approvers will make fewer mistakes because the report logic is staring at them.
Lock the pack
For each pay run, save four PDFs to the record: pay-run summary, STP preview, W1/W2 view, super accrued vs paid. For month-end, add super payable ageing and deductions ledger. For quarter-end, add payroll-tax wages by state. For EOFY, add RFBA and finalisation status. This isn’t bureaucracy; it’s how you avoid archaeology later.
Teach managers to read two charts
Give them overtime/penalties by person and leave balances/uptake. They’ll see where workload and fatigue are building, which cuts future payroll corrections and safety risk.
Small business? Here’s the lean version
If you’re under 20 staff and not chasing payroll tax, your essentials are: pay-run summary, STP preview, W1/W2 view, super accrued vs paid, and super ageing. Add YTD register for EOFY and you’re covered. Keep your payslip template aligned with Fair Work’s list (one working day, required fields) so staff stop emailing for basics.
The signal to the CFO
A tight reporting spine shortens BAS prep, lowers audit risk, and keeps employee trust high because payslips, STP and bank files all tell the same story. Your KPI is boring quarter-ends: W1/W2 agrees with prefill; super is paid and reconciled; finalisation hits 14 July without a scramble. That’s not luck, that’s the right reports, run on a schedule.
Bottom line
Build the mirrors first, STP Phase-2 preview and W1/W2, then layer the super, deductions, and liability views that keep cash and compliance tight. Use names that travel from payslip to STP. Reconcile accrued vs paid super like a hawk. Finalise STP by 14 July and keep your RFBA/FBT calendars straight. Do this and payroll stops being a source of surprises, and becomes a steady, defensible operation.