Revenue is to extend the pay and file deadline until 6pm tomorrow following problems with its online system ROS.
"With taxpayers and agents working towards a deadline of midnight tonight, 12 November, the ROS system has been experiencing very heavy usage volumes, with some 3,000 - 4,000 returns filed per hour throughout the morning," it said in a statement.
"These volumes caused intermittent downtime for some of those using the ROS system and while it was still possible to file returns, the volume of submissions were less than expected."
Revenue said its technical team refreshed the system and this resulted in ROS being unavailable for a period of time this afternoon.
Revenue has apologised for the inconvenience and extended the deadline for taxpayers who were filing their returns for last year through the system until 6pm tomorrow
It also claimed that ROS was operational again, although a spokeswoman later acknowledged that while submissions were going through, the system's performance was not at the level that Revenue would like it to be.
Many accountants have expressed frustration on social media at the ongoing issues.
One agent who contacted RTE News said he had lost six hours of working time today as a result of the problems.
Several others said that he had found the website has been unavailable for most of the day.
A number of taxpayers and agents have called for a further extension of the deadline beyond 6pm tomorrow.
This is the first time that Revenue has had to extend the ROS pay and file deadline in this way.
Over 500,000 self-assessed income tax payers filed returns this time last year and Revenue expect similar filing rates for the 2018 tax year.
Around 60,000 taxpayers still have to make their returns before tomorrow's deadline.