Decorated Australian war hero Ben Roberts-Smith has failed in a bid to win an injunction against Fairfax Media to prevent publication in Saturday's Sydney Morning Herald and The Age newspapers of detailed allegations concerning the former corporal’s behaviour.

Mr Roberts-Smith took action late Friday night in the Federal Court, arguing there had been a breach of confidentiality against federal law concerning an inquiry into Mr Roberts-Smith.

At 7.35pm, Justice Robert Bromwich ruled in Fairfax’s favour.

The 4500 word story, authored by investigative journalists Nick McKenzie and Chris Masters, plus Fairfax’s defence correspondent David Wroe, was published on Fairfax Media websites on Friday morning with plans for publication in Saturday’s editions of the Herald and The Age.

In court late on Friday, Arthur Moses, SC, for Mr Roberts-Smith suggested Fairfax Media’s reporters had committed a criminal offence by publishing confidential military information. He sought removal of the story from Fairfax websites and a ban on publishing the story on Saturday in print.

The story involved "wanton publication in breach of Commonwealth Law", in reporting details from an inquiry by the inspector-general into Mr Roberts-Smith while a member of the special forces. He said "there is no public interest in publishing material in breach of Commonwealth Law".

Sandy Dawson, SC, for Fairfax said the action was misconceived and should be against the Commonwealth not the publisher, noting that the "horse has bolted" given the story was published at 6am on Friday and "has been read by thousands".

"Where is the crime if the newspaper publishes?" asked Mr Dawson. "If there is a crime, it has already happened."

After the judgment, Mr Moses asked for the matter to be referred to the Australian Federal Police to see if there was "aiding and abetting" by journalists. Justice Bromwich said referrals from the Federal Court could only be made in the event of a determination by a court – and that would be a step too far.

Mr Roberts-Smith, who is one of three living recipients of the Victoria Cross for Australia, the nation’s highest military honour, issued an emphatic denial of the allegations, labelling them a "catalogue of lies, fabrications and misrepresentations".

He said early on Friday he would vigorously defend himself against the "malicious" claims.

“I do want to say today that I unequivocally deny any physical abuse of any woman at any time ever, and that I have not at any stage been interviewed by police about any purported complaint by any woman," Mr Roberts-Smith, now an executive at Channel Seven, said in a statement on Friday.

“I am deeply troubled that alleged evidence given on oath before the [Inspector-General of the Australian Defence Force] inquiry has been canvassed in the press and that Fairfax has allegedly accessed it. Not only is it illegal, it is unfair to people who haven’t given evidence and it has the potential to undermine the fairness of the inquiry."

The celebrated soldier said he was confident "direct witnesses will categorically demonstrate the falsity" of all the allegations made against him.

Prime Minister Malcolm Turnbull was asked on Friday about the story and allegations against Mr Roberts-Smith, saying: "I am aware of the allegations, complaints have been made to police and they will be dealt with appropriately,"

Mr Turnbull said. "I can’t make any comment on the specific matters because they are being dealt with by the police."