Australian Federal Police raid ABC headquarters at Sydney's Ultimo

Three officers entered the Harris Street building just before 11.30am. The plain-clothed officers were met by ABC security and staff in the lobby area of the ABC Ultimo Centre before meeting with lawyers for the broadcaster.

The raids are in connection with a 2017 report called "the Afghan files", based on leaked defence documents.

The police warrant names ABC reporters Dan Oakes and Sam Clark and news director Gaven Morris.

The story revealed incidents of Australian troops killing unarmed men and children, with the cases being investigated as potential unlawful killings.

The sensitive documents were marked as "AUSTEO" - Australian eyes only.

The raid comes the day after Australian Federal Police raided the home of News Corp journalist Annika Smethurst in connection with a 2018 story she authored concerning top-secret plans to expand surveillance of Australian citizens. Smethurst has not been charged with any offence.

It also comes days after a former Australian military lawyer charged over the leak of documents to the ABC was committed to stand trial in the ACT Supreme Court.

David William McBride, 55, is accused of theft and three counts of breaching the Defence Act, for being a person who is a member of the defence force and communicating a plan, document or information, an offence that carries and unlimited fine or prison time as penalty when heard on indictment.

ABC executive editor John Lyons, who is tweeting Wednesday's conversation between ABC lawyers and the AFP officers, said police have told them Wednesday's raid is not in connection to Tuesday's search of Smethurst's house.

"ABC lawyers tell AFP: We waive no rights, and reserve the right to take injunction against the warrant," John Lyons tweeted.

"The AFP tell us they are interested in 'certain things'".

In a statement, the Australian Federal Police said Wednesday's search warrant "relates to a referral received on 11 July 2017 from the Chief of the Defence Force and the then-acting Secretary for Defence".

The raids were "in relation to allegations of publishing classified material, contrary to provisions of the Crimes Act 1914".

"All AFP search warrants are authorised by a magistrate or an appropriate member of the judiciary. This is the result of supporting documentation or material being presented to the court which provides sufficient suspicion that a criminal offence has been committed," the statement said.

"No arrests are planned today as a result of this activity."

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 in a statement.

"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."

Prime Minister Scott Morrison on Wednesday said he was not troubled by a federal police raid on the home of Ms Smethurst, arguing all Australians must abide by national security laws.

2GB radio host Ben Fordham also revealed this week that he has been contacted by the Department of Home Affairs about his reporting, with the department investigating how he obtained "highly confidential" information about asylum seeker vessels.

Fordham said the department was seeking his co-operation with the probe, which could become a criminal investigation and "potentially" involve a police raid.

Journalists' union the Media, Entertainment and Arts Alliance said a second day of raids set a "disturbing pattern of assaults on Australian press freedom" and was an attack on the public's right to know.

"Police raiding journalists is becoming normalised and it has to stop," union official Marcus Strom said.

"These raids are about intimidating journalists and media organisations because of their truth-telling. They are about more than hunting down whistleblowers that reveal what governments are secretly doing in our name, but also preventing the media from shining a light on the actions of government."

Strom said the Coalition and Labor had together created a legal environment that was enabling a "politically motivated assault" on public interest journalism.

Centre Alliance senator Rex Patrick immediately hit out at the latest police raids, saying the ABC's investigation was clearly in the public interest.

"It appears this is the chosen week for a full-blown attack on freedom of the press in this country," he said.

Greens senator Sarah Hanson-Young called for an urgent inquiry into press freedom.

"Another day, another AFP raid on Australian journalists. This is a very worrying sign," she said.

"Australians deserve and have every right to know what our [government] is up to."