The union's boss, Angela Smith, said the AFP's latest draft enterprise agreement proposed cuts of up to $35,000 a year to 280 officers' remuneration.

The AFP planned to scrap a bonus for officers who worked at inconvenient hours.

The proposed cuts were first revealed via email to staff in December. Ms Smith, the Australian Federal Police Association's president, was disappointed the AFP had refused to ditch them in the latest draft.

"These people work extreme hours and it is a fairly significant cut to their wage," Ms Smith said.

"We've now got the help of the opposition to put pressure on the government, because we had no other choice."

Ms Smith would not reveal the base salary of the officers who would be affected, but said they worked in personal protection for the Prime Minister and Governor-General, as well as in witness protection, surveillance and counter-terrorism.

She said the draft agreement included clauses that had been left out of previous negotiations or never discussed with her association.

"This is not bargaining in good faith," she said.

Justice Minister Michael Keenan's spokeswoman said the matter was for the AFP and its staff.

"The government is confident negotiators will come to an agreeable position as soon as possible," she said.

The AFP said it did not want to debate the details of the proposal in a public forum.

"Proposals currently being negotiated were flagged with the AFPA and other independent bargainers in November 2016," it said in a statement.

"It should be noted that a scope order has been lodged with the Fair Work Commission that directly relates to this matter. To that end, it would be inappropriate for the AFP to comment further, until that matter has been determined. The scope order is due to be heard in April."

Ms Smith said the ongoing delays were due to the government's controversial workplace bargaining policy, which restricts the type of entitlements agencies can include in pay deals.

The policy also prevents government organisations, including the AFP, from offering pay rises unless they show they can fund them by making savings elsewhere.

Pay negotiations had been stalled for 15 months, prompting Ms Smith to write to Malcolm Turnbull seeking his intervention to stop the cuts. She also sought the support of Opposition Leader Bill Shorten and Labor justice spokeswoman Clare O'Neil this week.

A spokesman for Mr Shorten said the government was not doing nearly enough to protect the pay and conditions of AFP officers.

"We've been raising this issue in the parliament all week and the government's response has been pathetic," he said.

"This is a result of government policy - they can't wash their hands of this."

"It's time for the government to step up and protect the pay and conditions of the people who protect us.

Ms O'Neil said she would support the AFP and pressure the government to ensure the officers were getting the pay and conditions that they deserved.

The AFPA was calling for an annual 2 per cent pay increase for all members over three years, no changes to workplace conditions and a properly planned bargaining process to start early 2018.