Your ATO payment plan shows a missed instalment: what to check
Check the instalment and the plan status separately
You expected an ATO payment-plan instalment to be paid, but the account or a reminder now shows a problem. Start by checking the agreed amount and date, the payment record and the plan's current status. These are related questions, but they are not the same question.
Do not assume that seeing a bank debit proves the instalment was correctly allocated. Equally, do not assume that a reminder means every earlier payment has disappeared or that you know the plan's current status. Reconcile the records and ask the ATO or your agent to confirm what needs attention.
Keep the payment-plan agreement and the relevant reminder together. They give you a clear reference for the instalment being queried and the next conversation.
Source: ATO: Managing your payment plan
Trace the payment you expected to make
Find the relevant bank transaction or direct-debit record. Check its amount, date, reference and whether it was completed, rejected or returned. Compare it with the tax account rather than relying on the instruction you intended to send.
If the account does not show the payment you expected, keep the transaction details ready when you contact the bank, ATO or agent. Ask what information is needed to trace it and how to deal with the instalment while that is resolved.
Avoid making assumptions about a duplicate or replacement payment. Explain what has already been sent and seek confirmation of the next step, particularly if a direct debit and a manual payment may overlap.
Source: ATO: Payment plan estimator
Do not treat a tax refund as the scheduled instalment
A refund or credit may reduce the tax debt on your account. That does not necessarily mean the instalment you agreed to make has been satisfied. ATO payment-plan guidance says any tax refunds or credits you are entitled to will be used to reduce your tax debt through offsetting, but this will not replace the required instalment payment.
If you expected a refund to cover the next instalment, check the account and arrangement with the ATO or your agent. Separate the credit applied to the debt from the scheduled payment you were required to make.
Keep both entries in the reconciliation. This helps explain why the overall balance may have fallen even though the plan still shows a payment requiring attention. Do not cancel a scheduled payment solely because you see a credit.
Source: ATO: Payment plans
Check for other outstanding obligations
While investigating the instalment, ask whether other statements or payments are outstanding. The ATO explains that in addition to paying your payment plan instalments, you still need to consider your ongoing tax obligations. If you do not, your payment plan may default, making the full overdue balance immediately payable.
Keep those items separate from the disputed instalment. Identify the relevant period, account and action needed for each one, so an old payment query does not hide a new obligation that also needs attention.
If cash flow is the problem, update your forecast using the money available and realistic upcoming receipts. Include current obligations as well as the existing plan. This gives the ATO or your adviser a clearer picture of what the business can actually manage.
Ask what happens next and record the answer
Contact the ATO or your registered tax or BAS agent promptly with the agreement, account details and transaction records. Explain whether the issue is a missing payment record, an unsuccessful payment or an amount the business cannot afford.
Ask them to confirm the plan's current status and what action is required. If a change or replacement arrangement is needed, do not assume it has been approved until that is confirmed. Record the agreed amount, date, reference and any follow-up action.
If you have also received a formal notice, have the complete notice assessed promptly by an adviser with the relevant expertise. Keep its requirements separate from the payment-tracing discussion rather than assuming one conversation resolves both.