HMRC reported in April 2016 that both concessions that allowed to cancel penalties for late RTI submissions came to an end. However, it seems that HMRC may allow for some concessions to continue in some circumstances.
In order to help employers to avoid penalties for late submissions HMRC would not pursue charges if either the report was made not more than 3 days late (after salaries were paid) or if employers had no more than 9 employees on the payroll and were reporting just once a month regardless of when they actually paid salaries or wages.
Recently HMRC renewed the first concession (being late by no more than 3 days) and that applies retrospectively from April 2016. This has now been extended until 5 April 2017.
In some cases HMRC will not apply penalties for late submissions, for example, if you make an ad hoc payment to your employees outside of regular payroll and report it late. HMRC would also consider different reasons as to why RTI might have been submitted late.
