Coming just a day after a separate raid on the home of a News Corp political journalist, the search warrants related to the publication of stories in 2017 that accused Australia's elite special forces in Afghanistan of killing unarmed men and children.

The Australian Federal Police stressed the raids were unrelated, while Home Affairs Minister Peter Dutton was forced to affirm the independence of the AFP from government after Labor queried the timing of the raids.

The ABC raid took place a week after a former Australian military lawyer was committed to stand trial in the ACT Supreme Court charged over the leaking of documents now known as the "Afghan Files" to the ABC.

David William McBride, 55, was charged in March with a range of offences including theft, breaching the Defence Act and being a person who is a member of the Defence Force and communicating a plan, document or information.

It's understood the ABC and the AFP have been in talks about the search warrant since September, when it was first brought to the attention of the public broadcaster.

While both parties have been in discussions since then about a time at which to execute the warrant with minimal disruption to both parties, the negotiations inevitably culminated in the very public arrival of three AFP officers on Wednesday, which was the preference of the ABC.

AFP officers entered the ABC's Ultimo premises around 11.30am and spent the afternoon combing through nearly 10,000 documents projected on to a large screen. They left the building at about 8.20pm, taking some documents on USB sticks.

Three plain-clothes AFP officers and three digital forensics officers were accompanied by ABC lawyers and executive editor John Lyons, who live-tweeted the proceedings including photos of police sifting through the ABC's internal emails.

Mr Lyons said on Wednesday night the ABC and AFP had agreed on a two-week "hiatus" during which lawyers could challenge any documents seized under the warrant or the warrant itself.

A copy of the search warrant published by Mr Lyons showed it was signed off by a local court registrar, Martin Kane. It gave officers sweeping powers to access and seize notes, emails, footage, drafts, documents and other items related to the "Afghan Files" investigation.

The raid was swiftly condemned by the broadcaster's management, other media outlets, politicians, the National Press Club and unions. ABC managing director David Anderson called it "a serious development" that raised legitimate concerns about press freedom.

"The ABC stands by its journalists, will protect its sources and continue to report without fear or favour on national security and intelligence issues when there is a clear public interest," he said.

Mr Lyons said it was a "really serious escalation of the attack on the free media" which had significant consequences for Australian citizens.

"It's not just about the media - it's about any person out there who wants to tell the media about a bad hospital, or a school that's not working, or a corrupt local council," he said.

The ABC's news director Gaven Morris was named in the warrant alongside journalists Dan Oakes and Sam Clark.

In public statements, ABC editorial director Craig McMurtrie and Media Watch presenter Paul Barry said the police were pursuing an alleged breach of section 79 of the Crimes Act, which at the time of the article's publication related to the communication of official secrets.

That legislation did not contain exemptions for journalists, which meant it was "conceivable an ABC journalist could be charged," Barry said.

However, the AFP said both raids related to Part 6 of the Crimes Act, or section 70, which at the time only dealt with the disclosure of information by public officials. That suggested the individual journalists would not be pursued.

Labor's home affairs spokeswoman Kristina Keneally has asked for a briefing on why the raids were deemed necessary.

"Protecting our national security is complex work, but it always must have the right checks and balances," she said. "[Mr] Dutton must explain what he knew about these two raids."

Mr Dutton said he had no involvement in the AFP's investigations and was only informed of the raids after they had taken place. The AFP echoed that statement.

"Like all Australians, I believe in the freedom of the press," Mr Dutton said. "We have clear rules and protections for that freedom of the press and we also have clear rules and laws protecting Australia's national security."

Meanwhile the Greens have called for an inquiry into "declining press freedom", with media spokeswoman Sarah Hanson-Young calling the raid "a very worrying sign".

Global news outlets also voiced their concern about the raids, including the BBC's head of newsgathering Jonathan Munro, who said the development was "deeply worrying".

Warrant appears to give sweeping powers to seize anything - completely contrary to free media," Mr Munro said.

News Corp Australasia executive chairman Michael Miller expressed solidarity with the ABC and said national security and defence matters must be subject to proper public scrutiny.

The "Afghan Files" investigation relied on documents marked AUSTEO - "Australian Eyes Only" - many of which detailed "at least 10 incidents between 2009-2013 in which special forces troops shot dead insurgents, but also unarmed men and children".

The story was published in July 2017. It was not clear why the raid was executed nearly two years later, but Attorney-General Christian Porter said in relation to the News Corp raid: "There might be any number of reasons why things in an investigation happen some time after the investigation was commenced - that is not at all unusual".