Revenue has said that its online system ROS is back up and running after being offline for some time today.
Revenue had earlier said in a statement that it was aware of further difficulties with the ROS system after it also experienced issues yesterday.
"Revenue acknowledges the difficulties and frustration being experienced by taxpayers and agents who are continuing to try and file returns today and apologises for the inconvenience," it added.
"In light of the difficulties experienced with the ROS system over the last couple of days, a surcharge will not apply to any returns filed this week," it said.
It said that applies up to midnight on Sunday 17 November.
Revenue again said it sincerely apologised for the inconvenience caused.
The head of Revenue's Personal Division has said the problems with ROS did not arise as a result of a cyber attack.
Speaking on RTÉ's News at One, Declan Rigney said an investigation is continuing into the potential causes of the problems.
Revenue has confirmed that a surcharge will not apply to any Income Tax Self-Assessed returns filed online this week.— Revenue (@RevenueIE) November 13, 2019
That is, up until midnight on Sunday 17 November.
He said the issues are "complex and extremely technical", but he was confident they were not caused by "external factors."
He reiterated that that no surcharge will apply to any returns filed this week.
Yesterday, Revenue had extended the deadline for taxpayers who were filing their returns for last year and paying their provisional taxes for 2019 online until 6pm today.
It said these problems were caused by heavy usage volumes on the ROS system.
This caused intermittent downtime for some of those using the online system and while it was still possible to file returns, the volume of submissions were less than expected, it added.