Service went down onird.govt.nz soon after noon on what was one of the busiest times of the year.
Yesterday was the deadline for businesses to file monthly, two-monthly and six-monthly GST returns. It was also the last day to file the last instalments for the 2012 tax year.
The site was back up before 4pm. An IRD spokeswoman said it was unclear what caused the problem.
Deloitte Dunedin tax partner Peter Truman said he filed a GST return at 12.30pm and the site was slow at that stage.
Not being able to access the site did cause problems for tax practitioners. Taxpayers could file up to about 9pm but if the system was slow, that could also cause difficulties.
"As a tax practitioner I would like to see some administrative latitude from the IRD. If the network is up and running properly tomorrow, perhaps the IRD could treat returns filed then as filed on time."
The IRD website had gone down in the past but Mr Truman was unaware of it going down on such an important tax day.
However, Dr Clark told the Otago Daily Times the IRD site was "a ticking time bomb" and had crashed previously when IRD tried to update student loans.
"The current system is on life support. The system runs on 'ancient code' and the people who know the code are retiring. It is hard to maintain."
The Government had said it was going to spend between $1 billion and $1.5 billion to replace the First system over a period of several years.
Dr Clark said the logical solution would be to look at what Australia used and adapt that to New Zealand needs.
While acknowledging there would need to be a lot of "tweaks", Dr Clark said New Zealand was not the only Western country that ran a tax collection system.
It made sense to buy expertise rather than spending more than $1 billion building a system from scratch.
"A solution is years down the track and there is potential for things to escalate. I am anxious, we can't have a tax system that falls over."
New Zealand's tax system enjoyed a high degree ofconfidence but figures provided to the finance and expenditure select committee showed that confidence was falling, he said.
A website failing added to that picture.
"This is not small matter. It highlights a growing crisis," Dr Clark said.
