Officers arrived at the public broadcaster's Sydney headquarters with search warrants naming two reporters and the news director. The ABC has protested over the raid.
In a statement ABC Managing Director David Anderson said the police raid "raises legitimate concerns over freedom of the press".
"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."
According to the ABC, Wednesday's search is about the 2017 investigative series known as The Afghan Files which "revealed allegations of unlawful killings and misconduct by Australian special forces in Afghanistan".
The raid, which was the second to target journalists within 24 hours.
On Tuesday, police also raided the home of News Corp Australia journalist Annika Smethurst, who had reported on government plans to spy on its own citizens in a story that included images from a top secret document.
News Corp Australia, which is owned by Rupert Murdoch's News Corp, called the raid “a dangerous act of intimidation”.
(Excerpts from BBC News)