Inland Revenue will not penalise any traders who file late GST returns because of technical glitches that have affected its online payment system.
There have been numerous complaints from businesses and accountants about problems with IRD's MY-IR online system to pay GST.
Payments were due today, but accountants and traders have complained about not being able to log on to the system, or receiving demands for payments that have already been made.
IRD has said the problems were temporary glitches which had been fixed.
Commissioner Naomi Ferguson said a reasonable attitude will be taken with people missing the deadline.
"We will not apply late filing and late payment penalties for any GST returns due on June 28 if they are filed and payments made by Wednesday July 4."
"I sincerely apologise to our customers for any negative impact these service issues have had," she said.
Matt Shallcrass, a director at accounting firm Staples Rodway, said the rollout of new IRD systems had been premature, and the bugs had not been ironed out before they were commissioned.
"Inland Revenue is trying to use an off-the-shelf system geared for the European market, where no tax agents are used, and it's not suited for New Zealand."
Revenue Minister Stuart Nash said he was confident the system was now working well.
"[Inland Revenue staff] are working incredibly hard on this. Whenever they see a glitch, believe me, I hear about it, and people work overnight to fix it."
He said Ms Ferguson had assured both him and Finance Minister Grant Robertson that everything was under control.
"Thank you to the people of New Zealand for bearing with us, but IRD is going to be a much better organisation than it was pre-business transformation," he said.
"The system is going to make filing GST and payroll and all the other taxes a lot easier," he said
Mr Nash encouraged businesses to file and pay their taxes as soon as possible regardless of the deadline being pushed back.
"The systems are up and running. There's no excuse at the moment."