The controversial "stop the boats" policy of the Abbott government is in the sights of public servants in the Immigration and Customs departments as they move toward a strike over pay and conditions.

Unions representing workers from the soon-to-be merged departments will apply to the Fair Work Commission on Wednesday for approval to ballot their members on strike action.

The Community and Public Sector Union was cagey on Tuesday evening with details of the actions on the table but it is understood that elements of "Operation Sovereign Borders" and its controversial "on-water operations" to turn back asylum seekers' boats at sea, could be affected.

The CPSU confirmed that the proposed actions include walking off the job for up to 24 hours and was not confined to deskbound bureaucrats in Canberra and other capital cities.

If approved by the FWC, the fight looks likely to be taken to airports, ports, marine operations, mail centres and visa processing throughout Australian, its offshore territories and coastal waters.

Sovereign Borders, which the Coalition credits with stopping the flow of refugees arriving by boat on Australian shores, relies heavily on the efforts on land and water of workers in the two departments.

Restlessness is growing among the 5000 Customs officials, who have shown in the past they are prepared to strike over pay, and 8500 Immigration public servants who are still waiting for a pay offer nearly 10 months after their old enterprise agreements expired.

Department bosses have pointed out that devising one new enterprise agreement for the two departments, which will be merged in July, is complex and time-consuming.

Although there has been no pay offer, the union is not impressed with proposals around conditions which it says strips rights and entitlements while demanding longer working days.

Community and Public Sector Union national secretary Nadine Flood said her unions's members would stop short of any industrial action likely to threaten national security or endanger lives on the high seas.

"In keeping with our industrial action to date, our application explicitly states that workers will continue to perform any work related to safety of life at sea," the union leader said.

Immigration and  Customs are now the 14th and 15th government agencies taking or preparing for industrial action either in protest at what they say are low pay offers or trying to force their bosses to the negotiating table.

"Customs and Immigration staff stand to lose a lot more than they gain under the government's aggressive approach to bargaining," Ms Flood said.

"Customs and Immigration staff undertake valuable work protecting our borders and helping trade and the movement of people across our borders, often in dangerous and dirty conditions.

"If this government really values their work, as it so often claims, then why has it launched a vicious attack on their rights and conditions?"

Bargaining for the pay and conditions of around 160,000 public servants has been under way for a year but to date no agreement has been reached in any of the 117 agencies.

There is industrial unrest in Agriculture, Tax, Defence, Human Services, Veterans' Affairs, Environment, Employment, Geoscience Australia, CSIRO, the Australian Institute of Criminology, ABS and the Bureau of Meteorology, cover more than half of the Commonwealth's 159,126 public servants.