Australian Federal Police officers are raiding the ABC's Sydney headquarters over a series of 2017 stories known as The Afghan Files.
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 on hundreds of pages of secret Defence documents leaked to the ABC.
The search warrant named Oakes, Clark and the ABC's director of News Gaven Morris.
Three AFP officers entered the ABC first, followed shortly afterwards by three police IT technicians.
AFP officers served the ABC legal team with a warrant and are in talks with them about how the search warrant will be executed.
The AFP told the ABC they want 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.
"We are basically discussing a procedure we can all agree on to make this process as painless as possible," ABC lawyer Michael Rippon said.
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."
The raid comes one day after the AFP executed search warrants on the home of a News Corp journalist who had reported on secret plans to allow government spying.
The AFP released a statement saying no arrests were planned today 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" the statement said.
The ABC's Melbourne offices, where Sam Clark and Dan Oakes are based, have not been raided by the AFP.