An investigator with the Australian Federal Police (AFP) sought and acquired the call records of a journalist without a warrant, Commissioner Andrew Colvin says.

Key points: AFP officer was investigating a leak but didn't obtain the proper warrant

AFP officer was investigating a leak but didn't obtain the proper warrant Call records were accessed, not the content of those calls

Call records were accessed, not the content of those calls Journalist whose metadata was breached has not been informed

He said "human error" was responsible for the breach, which occurred during an investigation into a leak from inside the AFP.

The breach occurred earlier this year and an internal AFP review has been conducted, the Commissioner said.

Two days ago the matter was referred to the Commonwealth Ombudsmen, who will launch an audit of the breach next week.

The journalist whose metadata was accessed has not been informed, Commissioner Colvin added.

"What was accessed was the records of calls, not the content of those calls," he said.

"Just the fact of the existence of the calls in the first place.

"A result of this matter and as a result of us identifying this breach, we have been reviewing our internal practices and procedures to make sure they are as robust as possible."

The Commissioner said the material, which has since been destroyed, could not be "unseen" by officers investigating the leak.

"They'll need to consider in terms of next steps of the investigation what weight they put on what they saw but that material was accessed illegally," he said.

No disciplinary action has been taken against the investigator behind the breach, with Commissioner Colvin saying he did not believe there was any "ill will or bad intent".

Public should have 'full confidence' in metadata laws: AFP

Commissioner Colvin said the public could have "full confidence" in metadata laws and in light of the breach the AFP had "enhanced" internal procedures regarding access to phone records.

"We have raised the level of internal authorisation required for access to data of this type," he told reporters in Canberra.

"We are limiting the number of authorised officers who can approve access of this type.

"We are also re-rolling out and stepping up mandatory training to all investigators and authorised officers to make sure they are fully aware of their obligations under the Act."

The Commissioner said metadata was a "very common tool" used by AFP investigators but "extremely rare" that they were interested in a journalist's metadata.

Sorry, this video has expired Senator Scott Ludlam said authorities had been warned such breaches were possible.

Legal and media experts' have raised concerns about the protection of journalists under metadata retention laws, and in 2015 the Abbott government and Opposition passed laws making it harder for security agencies to access journalists' communication records.

Attorney-General George Brandis has not been available for comment on the matter but Labor frontbencher Anthony Albanese said any breach was a serious issue that needed proper investigation.

Greens senator Scott Ludlam said the breach demonstrated that the protections put in place for journalists were ineffective and raised questions about how all metadata was being handled.

He said the journalist who had their personal information accessed was owed an explanation and the AFP should be held responsible for the illegal breach, whether or not there was "ill will".

The WA senator, who was a vocal opponent of the data retention laws, also called on Labor to join the crossbench in voting to repeal them.

'The system has failed'

South Australian senator Nick Xenophon said he will question Commissioner Colvin about the breach at Senate estimates.

Guardian Australia journalist Paul Farrell said the AFP had accessed his metadata over a separate case and the breach revealed on Friday was "a shocking incident".

"The accountability measures in place, that is the Journalist Information Warrant that was introduced after the data retention amendments, is a complete farce and now it's been breached by the AFP without any kind of disciplinary process," he said.

Paul Murphy, the chief executive of the Media, Entertainment and Arts Alliance (MEAA) which represents journalists, said the metadata regime was an "attack on press freedom".

"Despite all of the requirements put in place before a Journalist Information Warrant can be granted, the system has failed," he said.

"This latest example shows that an overzealous and cavalier approach to individual's metadata is undermining the right to privacy and the right of journalists to work with their confidential sources."