Officers aboard two Cape Class and one Large Hull vessel have been put on high alert after colleagues worked alongside them while positive and asymptomatic since December 31.

The Community and Public Sector Union said some officers who tested positive were placed in detainee transportation accommodation and kept at sea, despite the quarters not having appropriate air-conditioning, basic amenities, power points, electricity or reliable WIFI to contact family or medical professionals.

Cape Class vessels typically hold crews of around 20 while Large Hull vessels can hold up to one hundred officers and support staff.

A Border Force spokesperson said it had complied with jurisdictional health directions and put place in appropriate safeguards underpinned by clinical health advice.

"The ABF has put in place robust safeguards to protect our staff, and the communities we interact with, from COVID-19," the spokesperson said.

The incidents have since been referred to the health and safety watchdog Comcare by the union for investigation.

The CPSU has lashed out at the Department of Home Affairs and its minister Karen Andrews for allegedly ignoring calls to address safety concerns, adding the situation could have been avoided.

Deputy national president Brooke Muscat said union members had been calling for changes since March 2020 and had first issued the department a Provisional Improvement Notice less than six months into the pandemic.

But in August 2021, a year after the notice was issued, the department had yet to introduce any specific protocols dealing with COVID-19, she alleged.

"The Department of Home Affairs has failed to adequately prepare for COVID on marine unit vessels," Ms Muscat said.

"At every turn they have rebuffed or ignored workers' calls for common sense protections when it comes to vaccination leave, crew testing, screening, and onboard logistics.

"For two years the CPSU members in the marine unit have been raising these risks, but due to inaction we have been left with no alternative but to seek a resolution through the regulator, Comcare."

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Border Force operates a total of eight Cape Class vessels around the country's maritime borders, meaning a quarter of the fleet has been affected.

A Border Force spokesperson said the law enforcement agency remained confident it could continue its role of protecting offshore borders.

"Our methods and policies have seen us successfully maintain a strong civil maritime fleet throughout the pandemic," they said.

Ms Muscat said Home Affairs secretary Mike Pezzullo needed to step in to ensure the safety of his department's officers.

"The Morrison Government must pay more than lip service to Australian Border Force officers; they must ensure that all workers on vessels are safe and that all workplace health and safety obligations are met," she said.

"Marine Unit officers do a dangerous and tough job, while being separated from their families for six months of the year.

"These officers need to be supported not left out to dry by a departmental secretary more concerned with his own ego than worker safety."

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