The department says that all the managers it drafted in to plug gaps at the nation's entry points were fully qualified to do the work safely and the Community and Public Sector Union got its facts wrong on a firearms incident at Darwin Airport during the strike.

The Canberra Times reported on Thursday that the union members were worried that dangerous individuals on watch lists, drug couriers, terrorism suspects and other criminal elements might have been missed as the department used untrained and inexperienced desk workers as "surge deployment" in a bid to keep the airport queues moving.

The CPSU also said an immigration manager, acting as a stop-gap for striking frontline officers, allowed a passenger who fronted up to Darwin airport with a gun in his bag to handle the weapon "to check if it was loaded".

But the Immigration Department, which did not initially respond to questions, released a statement on Thursday challenging some of the union's claims.

"Australian Border Force officers deployed under surge arrangements are not used as so-called 'strike-breakers'," a spokesman said in the statement.

"All officers deployed under surge arrangements have appropriate authorisation and training in accordance with the provisions of the Migration Act 1958, and follow correct procedures for processing airport passengers.

"All national security alerts were actioned appropriately and in accordance with operational requirements."

The department insisted that it always had the Darwin incident, where a passenger arrived at the airport to board a flight carrying a gun in a bag, under control and the union's claims were "totally incorrect".

"This activity was not related to protected industrial action with all ABF conduct fully compliant with normal business as usual export procedures," the statement says.

"The passenger was escorted to an inwards clearance area where two trained ABF officers verified the firearm and completed the restricted goods permit.

"The ABF officer who performed the firearms verification examination has current qualifications for Custodial Firearm Safe handling and is not a member of the Regional Command Management Team.

"The officers confirmed the firearm was disassembled in three pieces and at no point was the passenger asked to check if the firearm was loaded.

"There was no ammunition with the firearm and there was no risk to any member of the public or staff."

The department also hit out at the union's position on "strike breakers" saying the "surge deployment" was not such a radical departure from business as usual.

"Staff are routinely deployed between functions to meet operational requirements dependent upon available resource and priority," the spokesman said.

"The deployment of surge teams during school holiday periods is normal business practice.

"With protected industrial action occurring during the current holiday period, surge numbers have been larger than usual and have addressed the risk to the border and disruption to travellers that PIA would otherwise have caused.

"The majority of surge deployments were undertaken at a local geographic level with supplementation from other locations as required."