Hi Cathy1
You don't need to report the difference to the ATO. You report the super amount accrued when you process pay runs and declare through STP. The super funds report to the ATO when those contributions are paid. So the ATO can match what you should have paid with what you have actually paid.
If you haven't already it might be worth checking with the super funds how they deal with double payments and how they are reported to the ATO.
Please let me know if you need further help.
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