The public sector union says the sacking of three senior bureaucrats sends a blunt message to the Australian Public Service.
Soon after being sworn in as Prime Minister Tony Abbott announced he was dumping the three departmental heads of Industry, Energy and Agriculture in Canberra.
The CPSU's Nadine Flood says Mr Abbott is sending a clear signal.
"These are highly experienced people who are being sacked for having implemented the previous government's policy," Ms Flood said.
"They didn't create that policy, they weren't elected to do that, they were doing their job and we shouldn't see the public service being politicised with these sorts of sackings.
"It hasn't happened for some years and it's not a good sign."
Mr Abbott also outlined a series of changes to the structure of government departments and agencies.
More than 1,000 Canberra based staff from AusAID, Australia's overseas aid agency, will be merged into the Department of Foreign Affairs and Trade (DFAT).
Foreign Affairs will also take on responsibility for the overseas promotion of Australia as a tourist destination and the International Climate Change Division.
Responsibility for settlement services for refugees and migrants, along with aged care will move to Social Services.
While Customs and Border Protection Service will move from the Attorney-General's portfolio to Immigration.
The Coalition has already flagged it plans to cut 12,000 public service positions through natural attrition to save $5 billion from the Federal budget.
Ms Flood says the biggest concern is how those plans will be carried out.
"I think there are real questions over the Coalition's plans to cut 12,000 jobs by natural attrition and we're hearing across the public service that that may not be achievable and we may be looking at redundancies," she said.