Opposition leader Bill Shorten has dismissed calls from one of his MPs for an inquiry into the navy over allegations of asylum seeker abuse.

Labor has backflipped on its call for an inquiry into the navy over allegations of asylum seeker abuse, saying it has every confidence in the servicemen and women on the high seas.

Opposition leader Bill Shorten on Saturday issued a statement clarifying Labor was not seeking an inquiry into the navy’s alleged conduct, despite earlier comments to the contrary by an opposition MP.

“Our navy servicemen and women do an outstanding job on the high seas,” a spokesperson for Mr Shorten said in a statement to AAP.

“The opposition has every confidence in the skills and professionalism of our navy.”

Earlier shadow parliamentary secretary Matt Thistlethwaite said claims that sailors had burned asylum seekers should be treated with “healthy scepticism”, adding he had confidence in the navy.

But given the allegations were still being aired, he said an independent investigation would be appropriate.

“That’s the best way to vindicate the Australian navy,” he told Sky News on Saturday.

The suggestion sparked an explosive response from Immigration Minister Scott Morrison, who issued a lengthy statement blasting Labor as weak for supporting “baseless sledges” against the navy.

“Unlike the Labor Party, the government will continue to back our navy and customs personnel in the face of these wild, unsubstantiated allegations,” he said.

“Labor’s call for an inquiry, thereby legitimising these outrageous and unsubstantiated claims of torture, is a vote of no confidence by Labor in our navy and Customs and Border Protection Service.”

The opposition said the minister was being “hysterical”, and the culture of secrecy around border protection wasn’t making the navy’s job any easier.

Customs and Border Protection also issued a statement on Saturday, hosing down claims it would be launching fresh inquiries into the abuse allegations levelled at the sailors.

“Border Protection Command remains confident its personnel continue to act with the highest levels of professional conduct in a demanding and difficult environment,” the statement said.