The problem was reported on 22 June and customers are still reporting that the issue has not been fully resolved with those using the system complaining that confirmations are not being sent.

The system is part of the Government Gateway and is operated by the Department for Work and Pensions (DWP).

A Government spokesperson said: ‘We were aware of the issue affecting some online services on Monday. The problem was resolved that afternoon, and customers should have no problem using these services.’

HMRC told Accountancy that the latest service updates were available on its own service notifications page, but itt confirmed that although the system was up and running for submissions, there will still delays to confirmations, with slower than normal confirmation response times.

The HMRC website states: ‘We are aware that you may be experiencing a delay in receiving your acknowledgement to [PAYE] submissions made. Your acknowledgement will be sent once the service is restored. Please do not attempt to resubmit your submission. 

‘We are working with our IT partners to provide an urgent fix for the problem and apologise for any inconvenience caused.’

The deadline for PAYE submissions this month was 22 June.

Corporation tax filing has also been affected by the IT failure.

Under HMRC’s penalty scheme, the tax authorities will not charge a penalty if:

• your full payment submission (FPS) is late but all reported payments on the FPS are within three days of your employees’ payday (this applies from 6 March 2015 to 5 April 2016)
• for a new employer who sent first FPS within 30 days of paying an employee; and
• it is your first failure in the tax year to send a report on time (this does not apply to employers who register with HMRC as an annual scheme or have fewer than 50 employees for the tax year 2014 to 2015).

Updates to the PAYE service issue are available here

Updates to the corporation tax service issues are available here