The Prime Minister's department has agreed to accept a new pay deal.

About 1750 employees, or 81 per cent of the Department of the Prime Minister and Cabinet, voted in the ballot, returning a 78 per cent Yes-vote.

It should signal an end to a major industrial dispute that has lasted since the Abbott government, which has seen with two no-votes and a row largely due to the lack of dedicated domestic violence leave.

Getting a new deal was complicated by large wage gaps between public servants brought into PM&C in a massive expansion under Mr Abbott, and the better paid veterans of the department. 

PM&C employees could now get their first pay rise since 2013, but it will not include backpay due to a ban under the Coalition's hardline public sector industrial policy.

Before the Enterprise Agreement can come into play, it must be assessed by the Fair Work Commission in a process that can take up to eight weeks.