Parliament has admonished Labor frontbencher Stephen Conroy for calling into question the character of the general leading Operation Sovereign Borders.
The opposition's defence spokesman Stephen Conroy had used a Senate estimates hearing on Tuesday to accuse Lieutenant General Angus Campbell of being engaged in a political cover-up.
The accusation, later withdrawn by the senator, drew the ire of military chiefs and the federal government.
"I am pleased these accusations were withdrawn, but unfortunately once said, the shadow will linger," defence force chief David Hurley said.
Prime Minister Tony Abbott said it was unfortunate the senator had what could only be described as a brain snap.
Senator Conroy has resisted calls for an apology, insisting on Wednesday that he had no criticism whatsoever of military personnel carrying out government orders.
"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.
Later in parliament, the government sought to pressure Opposition Leader Bill Shorten over the issue, demanding he sack Senator Conroy as Labor's defence spokesman.
"He is unfit for that role," Foreign Minister Julie Bishop said.
She told Mr Shorten directly: "Having unleashed this dog of war it's time you put him back on the leash."
Junior defence minister Stuart Robert said the senator's performance was so bad that had he been in the army he would have been peeling potatoes.
It was left to independent MP Andrew Wilkie, a classmate of General Campbell at Duntroon, to initiate a parliamentary censure of Senator Conroy.
He called on MPs to admonish the senator for calling into question the general's character and integrity.
The government enthusiastically supported the motion as Mr Shorten and his senior colleagues huddled together to work out Labor's position.
In the end the opposition leader came out with all guns blazing, accusing the government of faux patriotism and wrapping itself in the Australian flag for political advantage.
The government was seeking to use the military as a stick to beat Labor about the head.
"Our military deserves better," Mr Shorten said.
The motion passed the House of Representatives on the voices and without Labor support.
