Over 11,000 Department of Immigration and Border Protection (DIBP) workers have rejected their third workplace deal, meaning the dispute will go to compulsory arbitration.

Industrial action at airports and Border Protection workplaces across the country by Community and Public Sector Union (CPSU) has been happening for months, as staff fight for their first pay rise since 2013, when their previous agreement expired.

The latest offer was rejected by 82 per cent of staff, with 11,840 registering a vote

That no vote was higher than the 81 per cent registered at the last workplace vote in March, but lower than the 90 per cent rejection from September 2015.

“This means that the Fair Work Commission will now determine your pay and conditions,” DIBP secretary Michael Pezzullo said in a letter to staff.

“This determination will be final and binding — you do not get a chance to vote on it.”

Arbitration will be a lengthy process, but the department says it will engage “in good faith”.

The Coalition Government has given departments little to work with, with a policy to offer only annual pay increases for public servants capped at 2 per cent, after a slight improvement from the 1.5 per cent cap limit imposed by former employment minster Eric Abetz.

CPSU national secretary Nadine Flood described the no vote as an “emphatic rejection of the fundamentally unfair and unreasonable deal”.

“DIBP staff are among tens of thousands of people across the Commonwealth public sector who are still fighting for a fair hearing over their workplace rights, conditions and pay,” she said.

“Public sector bargaining is a problem that isn't just going to go away.”

Commonwealth agencies including Defence, Human Services, Agriculture and the Attorney-General's department are still bargaining for new enterprise agreements.

A senate inquiry into the impact of the Government's workplace bargaining policy will be held on Friday.