© ABC News/Brendan Esposito
Australian Federal Police officers are seen meeting with ABC lawyers.

Australian Federal Police officers have left the ABC's Sydney headquarters more than eight hours after a raid began over a series of 2017 stories known as the Afghan Files.

Key points:

• The AFP said there would not be any arrests on Wednesday
• ABC managing director David Anderson said the broadcaster "stands by its journalists" and "will protect its sources"
• An AFP statement said the warrant was not linked to an AFP raid on a Canberra News Corp journalist's home on Tuesday

The stories, by ABC investigative journalists Dan Oakes and Sam Clark, revealed allegations of unlawful killings and misconduct by Australian special forces in Afghanistan and were based off hundreds of pages of secret Defence documents leaked to the ABC.

The AFP officers took with them two USB drives containing a small number of electronic files, which were sealed in plastic bags pending a review by ABC lawyers.

AFP technicians password-protected the files and police will be unable to access them until the two-week period of review is over.

The ABC's lawyers will now analyse the documents to determine any privilege claims. They are also assessing whether they will challenge the terms of the search warrant.

Three AFP officers entered the ABC building at about 11:30am, followed shortly afterwards by three police IT technicians.

AFP officers served the ABC legal team with a warrant and searched for information related to the warrant.

The AFP told the ABC they wanted to search through email systems in relation to the people mentioned in the search warrant and were searching "data holdings" between April 2016 and July 2017.

They searched for article drafts, graphics, digital notes, visuals, raw television footage and all versions of scripts related to The Afghan Files stories.

Thousands of items were found which matched search terms listed in the warrant.

ABC 'will protect its sources'

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

"This is a serious development and raises legitimate concerns over freedom of the press and proper public scrutiny of national security and Defence matters," he said.

"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."

ABC editorial director Craig McMurtrie described the raid as a "very unwelcome and serious development".

"This was outstanding reporting ... it was clearly in the public interest and sometimes difficult truths have to be told," he said.

"We will be doing everything we can to limit the scope of this and we will do everything we can to stand by our reporters."

Mr Morris, the ABC's director of news who is named in the warrant, said "journalism is not a crime".

"Our journalists do a really difficult job, I'm proud of what they do, they do it in the public's interest," he said.

"I'd say to all the journalists at the ABC and all the journalists across Australia, don't be afraid of the job you do.

"Stand up and be proud of it and continue to act in the public's interest knowing the stories you tell and the service you provide the community is a vital one for our democracy."

Media, Entertainment and Arts Alliance president Marcus Strom described the raids as "disturbing" considering they have taken place so soon after a federal election.

"It should chill the public as well as journalists," he said.

"This is not really about journalism and journalists. At the end of the day it's about the general public and its democratic right to know what the Government is doing.

"These raids are all about intimidating journalists and intimidating whistle blowers so that mistakes made by the Government, including potential crimes, by the military, remain covered up, remain secret, and don't fall in to the public domain."

'Not linked' to News Corp journalist's home raid

The raid comes one day after the AFP executed search warrants at the home of News Corp journalistAnnika Smethurst, who had reported on secret plans to allow government spying.

The AFP released a statement saying no arrests were planned on Wednesday and the warrant was "not linked to a search warrant executed in Canberra yesterday".

The search warrant was "in relation to allegations of publishing classified material, contrary to provisions of the Crimes Act 1914" and "relates to a referral received on 11 July 2017 by the Chief of the Defence Force and the then-Acting Secretary for Defence" the statement said.

A later statement from the AFP said Home Affairs Minister Peter Dutton was "not notified prior to the execution of the warrants".

"The AFP's actions have been independent and impartial at all times," it said.

"When the AFP receives referrals it assesses them for criminality and does not make value judgements on the issue instead identifying whether there has been any contraventions of Commonwealth Law, and when [sic] evidence as to whether the offence has been committed or otherwise."

In a statement, Mr Dutton said the AFP "conduct their investigations and carry out their operations independent from the Government".

"The AFP have an important job to undertake and it is entirely appropriate they conduct their investigations independently and, in fact, it is their statutory obligation.

"I have had no involvement in the AFP's investigation into these matters. Following the execution of each search warrant on 4 June and 5 June respectively, my office was informed that search warrants had been executed."

Opposition home affairs spokesperson Kristina Keneally said Labor had requested a briefing from Mr Dutton's office "to seek to understand why raids of such nature are warranted".

"Freedom of the press is an essential component of our democracy," she said.

The ABC's Melbourne offices, where Clark and Oakes are based, have not been raided by the AFP.

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