While people can still pay their bill through their bank the shut-down of the myIR service and contact centre means people can not currently check how much they owe.
Technology journalist Juha Saarinen said most transactions with the IRD were now through their online service.
"If you can't access that, and worse, the IRD contact centres, what are you supposed to do?"
He said dealing with the IRD was scary enough without having to deal with additional challenges.
"Luckily I have no urgent business with the IRD at the moment as far as I know (I can't log into the site and check that, obviously).
"For those who do, it must be very stressful and anxiety making, and I feel for people in that situation."
An IRD spokesman said customers with an outstanding debt due on the 7th could still pay through their normal method such as through their online banking.
"There will be leeway for those who make payments."
He said people who paid on February 7 would not incur any penalties and the department would be putting on extra staff to deal with anyone's concerns.
The spokesman said it had communicated with around 350,000 taxpayers since January about the shut-down and there had also been information about it on its website.
The GST upgrade is part of a multi-year transformation project designed improve the tax department's systems.
Greg James, deputy commissioner transformation for the IRD, said the GST changes were the first tangible benefits for customers of Inland Revenue's transformation programme, and were being delivered ahead of schedule and within budget.
"The new capabilities will enable customers to register for GST, register as a preparer of tax returns, amend GST returns and accounts, file and pay GST at the same time, set up payment plans, and track their GST payments and refunds - all online."
According to the IRD more than half of New Zealand businesses file their GST through Inland Revenue's secure online service myIR, or direct from their accounting software.
