The Immigration Department and Border Force officers will be joined by some quarantine and biosecurity staff, who will stop work for an hour.

The Community and Public Sector Union says some flights are likely to be delayed.

Workers say they are protesting against the federal government's protracted pay negotiations. Like most public servants, the striking staff have gone without a general pay rise for more than three years.

The strike follows several last year, though another planned 24-hour stoppage in March was called off at the last moment after the terrorist attack in Brussells, following a plea from Prime Minister Malcolm Turnbull for the unionists to reconsider.

Wage deals covering most of the federal bureaucracy expired in July 2014, when the then Abbott government's tough approach to wage bargaining came into effect.

The Coalition's policy forces government agencies to scrap some allowances and benefits, fund any proposed pay rises with savings and cap annual increases at 2 per cent.

Employment Minister Michaelia Cash said on Thursday it was "unfortunate" the union had resumed its strike campaign.

"This will cause harm to the public and involve a needless loss of pay for employees."

However, the union's national secretary, Nadine Flood, said the workers wanted to express the "frustration that continues to grow across the Commonwealth public sector".

"These people have been fighting for more than two years now as the Turnbull government has sought to strip their rights, conditions and take-home pay," she said.

"Across the public service, around 75 per cent of staff still don't have new enterprise agreements; that's more than 100,000 workers and their families who have now gone three years without a pay rise while struggling to hold on to basic workplace rights and conditions, particularly the ones that allow them to balance work with family commitments."

The union requested an "urgent meeting" with Mr Turnbull last week to resolve the dispute.

Ms Flood said the effects of the industrial action would vary from airport to airport, but said staff were "100 per cent committed to national security and their action will not compromise the safety of passengers in any way".

The union had agreed to more than 50 exemptions from the strike action, in areas such as counterterrorism and intelligence.