Staff have had to deal with angry calls from people unable to file returns.

Accountants have been threatening to file GST returns on paper after Inland Revenue suffered problems with its online systems.

Accountants around the country have reported widespread problems. Some said they could not log on to Inland Revenue's online MyIR tax system at all – although GST returns are due to be filed on Thursday.

There were also problems with GST returns being processed. Staff were told 10,000 phone calls to Inland Revenue were not answered last week.

One Inland Revenue employee who did not want to be identified said staff were subjected to angry calls earlier in the week – some accountants threatened to file their returns on paper because they could not get into the system.

READ MORE: Accountants fume over 'perfect storm' at Inland Revenue

Inland Revenue said on Wednesday it believed the problems with GST processing had been resolved.

"Initially the problems had appeared to affect only a few customers, it had been growing, but it was thought the problem was with customer log-ins. However some very specific customer feedback yesterday led IR investigations to the problem with the provider's network load rebalancer. That was quickly fixed by the provider," it said in a statement.

"IR apologises to affected customers and we understand how frustrating it has been in the lead up to the GST filing date. Most customers are now managing to file their GST returns, for example 18,000 did yesterday, which is around what we would expect.

"This hasn't impacted other types of tax, for example income tax or people seeking tax refunds. Last week there were over 700,000 logins to our online services, with 98.9 per cent within our service standard of six seconds."

Revenue Minister Stuart Nash said it was a "perfect storm" as people who were filing GST monthly, two-monthly and six-monthly all filed on June 28.

It was not an issue of computer systems needing to be changed, he said.

Spokesman Rowan McArthur said there were intermittent problems with the MyIR platform "but it is working. As problems arise they are dealt with as part of normal systems management."

National's revenue spokesman Paul Goldsmith was not impressed.

"The Minister's casual dismissal of concerns is particularly galling, given the extra pressure his Government has imposed on IR's systems by insisting that they also process the Best Start tax credit payments.

"Chartered Accountants Australia and New Zealand have raised the issue with IR but have yet to receive an explanation as to why the problem is occurring, how widespread the issue is and what steps are being taken to fix it.

"IRD collects $70 billion worth of taxpayers' dollars each year and we must have reassurance the system is working without glitches that prevent New Zealanders from fulfilling their tax obligations.

"The Minister needs to assure New Zealanders that IR is not in a state of crisis and is able to cope without causing significant disruption for taxpayers."

Craig Macalister, tax advisory partner at Crowe Howarth, said the GST problem was one of many the department had to contend with.

"There's been a number of ongoing issues with the change to the new system."

The department had also changed the way it processed tax credits and was automatically applying them to any money people owed - sometimes even if that amount had not yet fallen due, he said. Some clients had been confused by the change.

People were no longer being sent paper statements, so tax agents had to log in to the systems to check whether clients had received any communication.

But one tax agent could have thousands of clients and could not check every day for them all, he said.

"There are a lot of things that are causing tax compliance to be more difficult than it should be ... the smallest things are the hardest to resolve; getting an IR number, changing balance dates.

"They should be simple things to get done."