Labor leader Bill Shorten has told his defence spokesman the military head of the Government's border protection operation deserves his respect, the ABC has learned.

Stephen Conroy on Tuesday accused Lieutenant General Angus Campbell of a "political cover-up" in a Senate committee hearing.

The military commander in charge of Operation Sovereign Borders (OSB) was asked to explain why he had placed strict controls on information about "operational" or "on-water" incidents.

Senator Conroy compared the level of secrecy with that surrounding SAS activities behind enemy lines during the 2003 war in Iraq.

Lt Gen Campbell said he was offended by the remark and Senator Conroy was forced to withdraw it.

The Federal Opposition Leader has now spoken to both men.

It is understood Mr Shorten made it clear to Senator Conroy the military commander deserves respect, but did not demand he apologise.

The ABC has been told this has surprised and disappointed several Labor MPs, with one saying the party should not defend the indefensible.

Defence Minister David Johnston defended Lt Gen Campbell on Tuesday and called on Mr Shorten to "discipline" Senator Conroy.

Senator Conroy said on Tuesday evening it was the Government who should be apologising for placing the military in a highly partisan position.