Staff at Inland Revenue offices around the country have been told 30 percent of its workforce will go by 2021.
IRD, which employed about 6000 staff in 17 locations around the country, would reduce its workforce by 30 percent between 2018 and 2021, the Public Service Association (PSA) said.
Inland Revenue shut its offices and call centres between 1pm and 3.30pm this afternoon, so staff could hear about changes being made to the organisation.
Office staff were being give the rest of the afternoon off while call centres would reopen at 3.30pm, IRD said.
The PSA said restructuring from February next year could affect up to 4000 staff in various ways, but the impact had not been fully explained.
IRD Commissioner Naomi Ferguson told Checkpoint that staff already know about future job losses and today's announcement was about role changes for 3300 staff members.
Ms Ferguson said the organisation was changing to keep up with digital trends.
"We're creating some 900 new roles, mainly in management and specialist areas, and again, the 900 or so people affected will be able to apply for those roles. So this is not about a reduction in roles and jobs at this point, this is about changing how we work and giving people the opportunity to learn new skills as we transform," she said.
Labour's revenue spokesperson Michael Wood said the cuts were proof the National Party was not serious about multinational tax avoidance.
He described it as a whole-scale gutting, which he said would see the department lose experienced tax inspectors.
"We need a fit for purpose department that has sufficiently skilled and experienced staff to investigate things like multinational tax avoidance and preserve the integrity of the tax system and we are deeply concerned that these swinging cuts undermine that."
PSA national secretary Erin Polaczuk said staff also believed the changes would undermine the integrity of the country's tax system.
"The loss of expert staff and the lack of certainty for workers reapplying for more simplistically modified roles means that important regulatory changes to the tax system rest on very shaky foundations."
It was not known how many jobs would go in the first tranche of cuts, but changes would start to be made from February with the roll-out of the second stage of the IRD's computer system changes beginning a couple of months later.
The union said Inland Revenue staff expressed concerns during consultation that the organisation's business transformation plan would be undermined by the timing of its staffing changes, and could threaten the integrity of New Zealand's tax system.
"There's a lot of vague, corporate rhetoric and the language of restructuring being used by IRD management to hide the very real effects on expert staff," says Ms Polaczuk.
"Whether you call it 'streamlining' or 'cost-cutting', this plan could negatively affect our country's ability to pursue tax avoidance and compliance, as well as making life much more difficult for ordinary people seeking tax advice from IR call centres.
"Staff deserve fair wages for the work they do, an opportunity to occupy roles that fit their specific expertise, and decent treatment and engagement with their employer when major changes are made to how an organisation delivers its service."