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RNZ understands 35 to 40 jobs will be cut at the Commerce Commission, which is about 10 percent of its staff.
The ministry is the latest in a raft of ministries to announce job cuts.
They are part of the government's directive to public services to cut costs by between 6.5 and 7.5 percent.
In a statement, chief executive Adrienne Meikle said the commission has informed its staff there will be changes to its organisational structure and some roles as part of its bid to find cost savings.
Meikle said the commission remained focused on maintaining the delivery of all of its statutory functions.
Hundreds of workers could leave the Ministry for the Environment as part of cost cutting measures, the Public Service Association said on Monday.
The ministry has called for voluntary redundancies.
Ministry deputy secretary of business transformation and services Laura Dixon confirmed "expressions of interest" for voluntary redundancies from permanent staff had been called for.
Meanwhile, about 30 science and engineering jobs at Callaghan Innovation are set to go as part of a "strategic reset".
Callaghan is one of New Zealand's largest research organisations.
The Public Service Association's assistant secretary Fleur Fitzsimons said the Commerce Commission's job cuts were very concerning "given the whole important watchdog role the Commerce Commission plays within the whole government sector".
The total number of job losses were going much deeper than what political parties described during the election campaign, she said.
The union believed the latest round of public sector job cuts for the Ministry of the Environment and Callaghan Innovation were an attack on science.
"It's a really dark time for science ...both of these agencies play such an important role in preparing New Zealand for the impacts of climate change but also on our work in reducing emissions, which the government says it wants to focus on in these targets they've released."
The cuts did not make any sense, she told Morning Report.
Fitzsimons said the government was meant to be taking a detailed, line-by-line approach to the cutbacks in expenditure at the ministries, but there was no evidence of that happening, she said.
The PSA was also concerned about looming cuts at NIWA which have yet to be announced.
"It's another random cut by this government with no evidence base and it's going to mean New Zealanders pay the price in the longterm."
