The public sector union fears more jobs will be lost in Canberra as the Customs and Border Protection Service cuts its staff. Along with 38 positions in the intelligence division, up to 20 frontline staff will go in Sydney.
The cuts are part of the customs response to federal government budget cuts that will result in 190 positions going this financial year.
The Community and Public Sector Union says the cuts to operational staff at the customs national intelligence-gathering unit and at Sydney Airport could expose the country to greater security risks and lengthen wait times for travellers.
CPSU national secretary Nadine Flood said customs has told staff 38 positions in its intelligence division are to go nationally.
''The customs intelligence division does have staff in Canberra, as it does in other cities around the country, so we can't rule out that there won't be cuts in the national capital,'' she said on Friday.
''The intelligence division is the eyes and ears of customs. Regardless of whether they are located in Constitution Avenue or in regional Australia, these cuts are bound to have an impact on security.
''As it stands, customs has not put forward a formal proposal and we are seeking answers from them urgently.
''Given the cuts by customs are touching every corner of the country, from Townsville and Cairns to Tasmania and Perth, it is reasonable to assume that Canberra is unlikely to be spared some of the pain. But as I said, we are seeking answers from customs.''
Customs operations staff were already working harder with fewer resources, and the latest tranche of cuts would put them under greater pressure, Ms Flood said.
''Sydney Airport is the nation's busiest gateway and yet here is customs wanting to reduce its frontline staff by 4 per cent, at the same time putting staff under constant pressure to meet an increasing number of passengers,'' she said. ''This will have a direct impact on how they do their job, whether that's checking bags or passports or helping tourists fill out forms.
''Now is not the time to be taking away resources from customs. In the current environment, customs workers need all the backing they can get.''
Opposition customs spokesman Michael Keenan said the union had confirmed the damage the staffing cuts were doing to national security.
''Nadine Flood said today that the work that these customs staff do is absolutely crucial,'' he said.
''Since Labor came to office, they have slashed millions in funding from customs and cut a total of 750 staff, hindering the frontline agency's ability to protect our borders.
''Labor has left our frontline border-protection agencies so ill-equipped it is no wonder that illegal weapons, drugs and other contraband are making their way onto our streets and into our community.''
A response was sought from Customs and Border Protection.