The Inland Revenue has apologised for a glitch which caused problems for people trying to lodge GST returns online and says the issue is now fixed.

The problems came to light after the accountant's association spoke out about its members experiencing a number of problems, including slow access to the IRD's online service myIR and filing GST returns.

John Cuthbertson, tax leader at Chartered Accountants Australia and New Zealand, said its members had been reporting slow access to the myIR system and problems loading returns for two weeks.

"It is when they access myIR things are very slow. People trying to file their GST returns early have been able to do it, but have had problems with lodging it. There has been a whole range of things like that."

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He said the problems were compounded by the phone system being already busy at this time of year.

The association met with the IRD last week to discuss the issues but Cuthbertson said the department had been unusually "quiet" on the problems.

This morning the IRD released a statement saying it believed the problems with its GST processing system were now resolved and blamed it on a network load rebalancer at the Inland Revenue's telecommunications provider.

"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."

Inland Revenue apologised to affected customers.

"IR apologises to affected customers, we understand how frustrating it has been in the lead-up to the GST filing date."

It said most customers were now managing to file their GST returns, with 18,000 filing yesterday - around the typical number it received.

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But it urged anyone who may have problems meeting the filing deadline because of the problems to get in touch.

"If any customer has difficulty meeting their GST filing date because of issues with our online services, let us know, and we'll be reasonable about that."

The spokeswoman said the problems appeared to be isolated to those trying to do GST returns.

"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 6 seconds."

She said the problem also did not affect Best Start - the government's new baby payment, which would be processed as planned from July 1.

But Matt Shallcrass, a partner at accounting firm Staples Rodway, said it was not just GST where it was seeing problems.

"We are seeing isssues across the board."

Shallcrass said other issues were clients who had paid their tax only to receive a reminder for it. Some ended up accidentally paying twice and then it was a struggle to get the overpayment back.

In another case the penalties for not paying fringe benefit tax had been charged incorrectly.

He said the issues had been building up for the last 12 months but had got worse in the last six months and he put it down to a lack of testing when it came to changes the Inland Revenue was making as part of its business transformation project.

"There are lots of things causing general frustrations and adding to the cost of doing business."

Shallcrass believed the IRD needed to be more careful before sending out correspondence and blamed some of the problems on a lack of quality control.

The issues come as Inland Revenue staff prepare to walk off the job.

More than 4000 Inland Revenue Department and Ministry of Business, Innovation and Employment staff will go on strike next month.

Staff at both agencies are due to strike for two hours on July 9 and July 23.

"Our members are very reluctant to take this step, but they feel they have no choice - and the level of support in the vote shows the level of frustration," Public Service Association [PSA] national secretary Glenn Barclay said.

Earlier this week the PSA claimed Inland Revenue's IT system cannot process the new Best Start tax credit which kicks in next week as part of the Government's Families Package and it would have to be done manually.

"Our members take their jobs very seriously and they're trying desperately to keep the system on track while IR presses ahead with its Business Transformation project which will see 1 in 3 staff let go by 2021.

"It starts on 1 July, and members are told they will have to process this manually, drastically increasing their workload," PSA national secretary Erin Polaczuk said.

"To have all this happening while the employer refuses to consider a modest across-the-board pay increase is deeply upsetting to our members."