Both parties have agreed to a two-week hiatus during which the warrant - targeting reporters Dan Oakes and Sam Clark as well as news director Gaven Morris - or documents handed over under the warrant, can be challenged.

Wednesday's raid in Ultimo concerned ABC news reports in 2017 that revealed Australian defence personnel may have committed war crimes in Afghanistan.

It came a day after AFP officers searched the Canberra home of News Corp Australia journalist Annika Smethurst over a 2018 story detailing an alleged government proposal to spy on Australians.

ABC head of investigative journalism John Lyons on Wednesday said he'd "never seen an assault on the media as savage as this one we're seeing today".

The warrant allowed the AFP "to not just take and seize but to delete and to change official ABC documents", Lyons told ABC TV.

The ABC is assisting forensic digital officers sort through the material but could yet refuse to hand over any documents and instead contest the warrant in court.

The AFP and the ABC agreed there would be a two-week hiatus, during which any documents handed over under warrant can be challenged, or the entire warrant can be challenged, Lyons posted on Twitter on Wednesday evening.

Both parties have gone through about 70 per cent of the documents in question, and the broadcaster's lawyers had many taken out on the basis of legal privilege, Lyons wrote.

Home Affairs Minister Peter Dutton said he had no involvement in the AFP investigations and his office was only informed after the two warrants were executed.

The AFP insisted there was "no link" between the ABC and Smethurst raids and confirmed Mr Dutton "was not notified prior to the execution of the warrants".

"Both, however, relate to separate allegations of publishing classified material contrary to provisions of the Crimes Act which is an extremely serious matter that has the potential to undermine Australia's national security," an AFP spokesperson said.

ABC managing director David Anderson said it was "highly unusual" for the national broadcaster to be raided.

"This is a serious development and raises legitimate concerns over freedom of the press," Mr Anderson said in a statement.

The ABC stood by its journalists, would protect its sources and continue to report "without fear or favour" on national security and intelligence issues, he added.

Wednesday's raid was in relation to a July 2017 story that revealed hundreds of pages of secret Defence Force documents gave "an unprecedented insight into the clandestine operations of Australia's elite special forces in Afghanistan including incidents of troops killing unarmed men and children".

The ABC reported at the time some of the cases were being investigated "as possible unlawful killings".

Federal Labor said it had requested a briefing through Mr Dutton's office asking "why raids of such nature are warranted".

"Freedom of the press is an essential component of our democracy," opposition home affairs spokeswoman Kristina Keneally said.

News Corp labelled Tuesday's raid on Ms Smethurst's home "a dangerous act of intimidation towards those committed to telling uncomfortable truths".

It backed the national broadcaster on Wednesday with executive chairman Michael Miller stating "we support the ABC's concerns over freedom of the press and proper public scrutiny of national security and defence matters".

The Australian Press Council said the police raids could have a "chilling effect on journalists and may intimidate them from pursuing legitimate stories in the public interest".

The media union said the raids were an attack on the public's right to know.

Australian Associated Press