Australian touring company APT has launched a legal case which could potentially strike out a government order that all cruise ships leave Australian waters as soon as possible.

APT, which has a number of small boutique ships as well as river vessels in Europe and Asia, has asked the federal court to rule out part of a determination made on 27 March by health minister Greg Hunt, that has ordered foreign-registered vessels out of Aussie waters.

The company’s Caledonian Sky is currently in Darwin’s Harbour, but the vessel is registered in the Bahamas.

In a brief hearing held by video link on Tuesday, judge Angus Stewart said that an order of the type sought by APT “potentially affects all foreign cruise vessels in Australian territory and not only the particular vessel otherwise directly affected by this case”.

APT notified the attorney general of the lawsuit and it was before the court on Wednesday.

Border Force commissioner Michael Outram has given an undertaking to the court to not remove the Caledonian Sky or its crew from Australia until 5pm this afternoon.

He said that he was “working through” the APT case.

“But let me make clear the government’s policy intent here is that all cruise ships that are in Australian waters that are not flagged or registered in Australia are to depart Australian waters and we’re working to achieve that outcome,” he said.

The ship caters for 114 passengers, and mainly sails luxury cruises in the Kimberley.