HM Revenue and Customs is changing the systems it uses to support its Real Time Information (RTI) system, and is delaying fining employers who don't fully adopt the replacement PAYE system.
HMRC originally said it would start charging interest and fining firms for not filing and making payments in time under RTI from 6 April.
Companies have to integrate their financial systems with RTI in order for them to make those payments to HMRC.
Despite previously saying the vast majority of firms were RTI-compliant, HMRC now says: "RTI is a big change and HMRC and some employers are continuing to learn.
"Having listened to customer feedback, HMRC has decided to stagger the start of the new in-year late filing and payment penalties, to give employers more time to adapt to reporting in real time."
The new timetable will be:
April 2014 - in-year interest on any in-year payments not made by the due date October 2014 - automatic in-year late filing penalties
April 2015 - automatic in-year late payment penalties
At the same time, HMRC is changing its systems to cope. It says it has worked closely with the Department for Work and Pensions (DWP) to ensure that RTI will support the operation of the government's new Universal Credit system, which brings together means-tested in and out-of-work benefits.
The Universal Credit system has already experienced IT problems and is behind schedule.
HMRC director general for personal tax, Ruth Owen, said: “The introduction of RTI is going extremely well for the majority of employers but there are still some who need a bit of time to adapt fully to the changes.
"This additional time will give us the opportunity to ensure that improvements to our internal systems are working, to learn from them and to provide better customer support to employers who need more time to adapt.”
Forthcoming changes to HMRC systems include, from April 2014, HMRC will introduce a new RTI "Late Reporting Reason" data item. This will allow employers to tell HMRC why they are submitting data late – for example, if they are correcting an earlier submission.
HMRC says it is also enhancing its internal systems to include additional safeguards, for example, to automatically correct some types of common employer errors.
HMRC will also suspend the issue of electronic generic notification alerts for late payment and non filing until April 2014.
HMRC will still issue late payment penalties manually for 2014-15, as it has done in previous years.
Employers will be able to see the amount of interest being accrued in their online tax account, but HMRC won’t seek payment until the debt is settled.