The Morrison government has seized on a new court judgement to argue it will “open the floodgates” for the medical evacuation of offshore asylum seekers and demanded Parliament repeal the legislation.

The Federal Court has found that the Home Affairs Department was wrong to reject an Iraqi asylum seeker’s claim for transfer on the grounds the doctor had not examined the individual in person or by teleconference.

It appears to set a new precedent that asylum seekers could secure advice that they need to be brought to Australia by a doctor simply examining their case notes.

• Read more: ‘What is Peter Dutton really trying to say?’

Justice Mordecai Bromberg found department secretary Mike Pezzullo erred when he did not inform the minister of the asylum seeker’s application for a medical transfer on the grounds the advice was not offered after an examination of the man.

“There is nothing to support [the Home Affairs Secretary’s] underlying proposition that an assessment without personal engagement would have been regarded by Parliament as not warranting consideration for approval,” the judgement finds.

Home Affairs Minister Peter Dutton with Sri Lanka’s navy commander Piyal De Silva, and the head of Operation Sovereign Borders Major General Craig Furini. Photo: AAP

Home Affairs Minister Peter Dutton warned the result was “a mess.”

“This is a mess entirely of Labor’s making,” Mr Dutton said.

“They voted for this law not having any idea of the consequences.

“The Australian people voted for the Coalition because we keep the borders secure and we will be abolishing this Bill or the boats will restart.”

• Read more: ‘All roads lead to Dutton’

The Morrison government’s hopes of overturning the Medevac laws appeared to be undermined on Sunday when Mr Dutton conceded that “only just over 30” refugees had been brought to Australia under the new laws.

It appears to be less asylum seekers than were brought to Australia under the old laws during the same period.

Prime Minister Scott Morrison had repeatedly warned the new legislation would “open the floodgates” to Australia.

He also re-opened the Christmas Island detention centre to deal with the influx at a substantial cost totalling millions of dollars.

Mr Dutton said on Sunday that no asylum seekers had subsequently been transferred there.

Labor and the crossbench voted for the medevac legislation, which bolstered the role of GPs in starting a formal process for the minister to consider a transfer.