Do the new RTI penalties apply to RTI adjustments filed for periods before 6/10/14 or earlier year updates?
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Code H
If you mark the Late Reporting Reason (scroll up a bit) as H - Correction to earlier submission - on your amending FPS, then hopefully HMRC will not impose a late filing penalty.
However, why are you submitting an amending FPS after the pay day? HMRC's preferred method of correcting errors is to adjust the YTD figures on the next pay period's FPS. Do that and you avoid all risk of a late filing penalty.