Staff will vote on industrial action as unions resist federal government-owned Airservices Australia's move to drop entitlements from a new enterprise agreement.

Professionals Australia, which represents engineers and scientists at the 3700-strong agency managing the nation's airspace, said staff had been patient and that the decision to hold a protected action ballot was not taken lightly.

Airservices Australia would cut its Employee Grievance Board, an internal mechanism to resolve workplace disputes, forcing staff to take disputes directly to the Fair Work Commission in a move that could create more work and costs, the union said.

Agency-funded study relating to work could also disappear under the proposed deal, union ACT organiser Brendan Forde said.

"For our members, performing highly technical and professional roles which require periodic and often expensive study and training, this change will directly impact upon how they perform their jobs,” he said.

“Our members are open to considering changes to the enterprise agreement that improve the effectiveness and efficiency of Airservices. But the changes won’t achieve this."

Airservices Australia said it was seeking a simplified enterprise agreement that aligned with the federal government’s workplace bargaining policy.

"We have been negotiating in good faith since August 2017 and our aim is to have a new agreement in place as soon as possible," a spokeswoman said.

Among possible actions staff could take are work stoppages and wearing campaign materials.

Unions and Airservices do not expect proposed industrial action will disrupt any critical operational or safety services.

Professionals Australia told Fair Work it asked the agency to start negotiations in February 2017 but waited six months for talks to begin, leaving a month before the old agreement expired.

The Community and Public Sector Union, which is also sending ballots to members at the agency, has told them the Coalition government's bargaining policy has made Airservices stall and delay at the negotiation table.

"No worker in Airservices needs to be reminded that it has been nearly 12 months since you and your colleagues received a pay rise," it said.

"Airservices’ delaying tactics are unacceptable and cannot continue without consequence. The majority of CPSU members believe it is time to increase pressure on the government and Airservices to deliver an agreement which maintains your conditions, rights, entitlements and includes a fair pay increase."

Mr Forde said Airservices had recently negotiated agreements with its air traffic controllers and aviation fire fighters which were comparatively fair and reasonable.

"Our members simply want to be treated the same. All they want is a fair and reasonable enterprise agreement.”