Prime Minister Tony Abbott has called on a senior Labor senator to apologise for his “brain snap” when he accused an army general of being engaged in a political cover-up.

Opposition defence spokesman Stephen Conroy was forced to withdraw the accusation against Operation Sovereign Borders commander Angus Campbell during a Senate estimates hearing on Tuesday.

“I think that uniformed officers of our country should be treated with our deep respect,” Mr Abbott told reporters in Canberra on Wednesday.

“It was unfortunate that Senator Conroy had what can only be described as a brain snap.”

Mr Abbott said if the senator wasn’t “big enough” to apologise, Labor leader Bill Shorten should have a word in his colleague’s ear.

Senator Conroy insists it is not for him to apologise.

“It is the government who should be apologising to the Australian public,” he told reporters, citing the death of an asylum-seeker at the Manus Island detention centre.

Mr Shorten said Labor’s “beef” was not with the military, but their “political masters” in the government.

“We don’t support the federal government using our military in a cloak of secrecy and not being upfront with the Australian people,” he said.

Australian Greens MP Adam Bandt said it was disappointing the military was implicated in a cover-up when the matter was ultimately the responsibility of Immigration Minister Scott Morrison.

Assistant Defence Minister Stuart Robert said Lieutenant-General Campbell was a decorated officer and should be lauded for stopping the boats and not subjected to grubby attacks.

“Be a man, Conroy and apologise,” he told reporters.

Independent MP Clive Palmer said he understood Senator Conroy’s frustration over government secrecy about Operation Sovereign Borders.

“It’s very disappointing the military have been brought into what is a political fight,” he said, adding the military should not be used for that purpose.

Liberal senator Chris Back joined calls for an apology, saying personal abuse was no substitute for intellectual rigour.