Australian Federal Police (AFP) officers who raided the ABC's head office were searching for evidence — including fingerprints — to prove that an ABC reporter had committed criminal offences, court documents have revealed.

Key points: The warrant related to stories of alleged unlawful killings by Australian special forces in Afghanistan

The warrant related to stories of alleged unlawful killings by Australian special forces in Afghanistan About 100 files were seized in the raid and sealed by the AFP

About 100 files were seized in the raid and sealed by the AFP Managing director David Anderson said the ABC would challenge the constitutional validity of the warrant

An application by the ABC to the Federal Court of Australia said the AFP obtained a search warrant authorising them to search for evidence to prove a suspicion that investigative journalist Dan Oakes had allegedly committed the offences of receiving stolen goods and unlawfully obtaining military information.

The warrant authorised the AFP to search for and record "fingerprints found at the premises" and to take samples from the ABC for "forensic purposes".

It also authorised the AFP to "add, copy, delete or alter other data … found in the course of a search".

The AFP raid on June 5 related to a series of stories by Oakes and producer Sam Clark known as the Afghan Files.

Acting AFP Commissioner Neil Gaughan said the AFP is "a strong supporter of press freedom". ( AAP: Lukas Coch )

The stories detailed the alleged unlawful killings of unarmed men and children by Australian elite special forces in Afghanistan and were based on hundreds of pages of leaked documents.

On Monday, the ABC launched a legal challenge to the warrant used to raid its Sydney headquarters, seeking a declaration from the Federal Court that the warrant was invalid and the search and seizure of more than 80 items relating to the Afghan Files was unlawful.

The ABC is also seeking an injunction restraining the AFP from accessing any of the seized materials and an order that the items be immediately returned to the ABC.

The application to the Federal Court states, "the Afghan Files were reports in relation to government and political matters of the highest public importance".

"The sources of information relied on in preparing the Afghan Files included information provided to Oakes by informants in circumstances where Oakes had promised the informants not to disclose the informants' identity," it adds.

"The Afghan Files state that they were based upon information provided by such sources."

The application argues that the terms of the warrant were too vague and broad and the decision to issue the warrant was "legally unreasonable".

AFP officers talk with ABC lawyers during the June 5 raid. ( ABC News: Brendan Esposito )

It also argues that the AFP's decision to seek and execute the warrant was unreasonable because of "the importance of the protection of sources" and "the public interest in investigative journalism and the implied constitutional freedom for the reasonable discussion of government and political matters".

Managing director David Anderson said the ABC was also challenging the constitutional validity of the warrant "on the basis that it hinders our implied freedom of political communication".

Mr Anderson said it was important that Australians be advised of the court action and of the ABC's determination to defend its journalists and the crucial work they did to inform the public.

On the day of the raid, AFP officers were joined by specialist computer technicians and searched the databases with the ABC's legal team for more than eight hours.

From thousands of items found using keyword searches in the files, only about 100 were ruled as relevant to the AFP's warrant.

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Just before 8:30pm officers exited the ABC headquarters, taking with them two USB drives containing a small number of password-protected electronic files, which were sealed in plastic bags.

Mr Anderson said the AFP had given an undertaking not to access the seized files until the court challenge was determined.

"Rest assured, though, that the ABC will be using every avenue over the next few weeks to defend the actions of its journalists and to seek legislative changes that protect the media's ability to report on matters of public interest," Mr Anderson said.

Mr Anderson said he would be speaking at the National Press Club on Wednesday alongside media executives from News Corp Australasia and Nine.

"Collectively and individually, we are committed to working constructively with the Government to address weaknesses in the legal protections for journalists and whistleblowers and to push for meaningful, urgent reform," he said.

Oakes and Clark released a joint statement.

"We appreciate the support we've received from the ABC, our colleagues and the wider community," they said.

"At this stage, while the AFP's investigation into our journalism continues, we are unable to say anything further."

A full court hearing is not expected until late July or early August.

The AFP also raided News Corp journalist Annika Smethurst's home the day before the ABC.

News Corp confirmed it would seek to set aside the AFP's warrant that allowed the police to search Smethurst's home.