HMRC's decision to set up a specialist team to look at issues with PAYE reconciliation errors under the new RTI system has been welcomed by CIOT, which says a range of problems are adding to the workload for some employers.

HMRC has admitted that it is experiencing ongoing discrepancies between the amount of PAYE it believes employers should pay and what companies think they owe. It has updated its guidance, and created a dedicated team to work with employers to identify why this is happening.

Tina Riches, CIOT director, technical, said: 'We are aware there have been problems with PAYE reconciliation and these appear to be happening for a host of different reasons. The most common ones have been sorted, but there are now a number of individual cases which need examining to find the underlying problem.'

Examples reported by CIOT members include a case where a payment made by an employer for PAYE and NICs was wrongly allocated by the HMRC system, so that there appeared to be an overpayment of one amount due and an underpayment of the other.

There have also been instances where payments made to employees who have recently left a company and received a P45 have been treated under RTI as if the individual is a new starter at that company, because the earlier record has been closed. As a result, tax figures are duplicated.

Riches said: 'Each of these queries takes quite a while for the employer and HMRC to whittled down to find out exactly what the problem is. We've had a number of cases reported to us and they are all different.'

HMRC has stated it will be updating RTI guidance regularly to reflect what it learns about PAYE reconciliation discrepancies. It will also be providing fixes to the system where necessary.

'They definitely need a specialist team on this, because some employers are spending a lot of extra time sorting discrepancies out,' Riches said.