Police searched the home of a News Corp journalist on Tuesday, sparking alarm.
The BBC said it was "deeply troubling" for a broadcaster to be searched.
The leading journalists' union in the country said the two raids represented a "disturbing pattern of assaults on Australian press freedom". Other unions and human rights groups also condemned the actions.
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."
ABC News director Gaven Morris defended the two journalists who were named along with him in the search warrant.
The police action is related to articles about alleged misconduct by Australian forces in Afghanistan.
According to the ABC, 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 broadcaster said the series was "based off hundreds of pages of secret defence documents leaked to the ABC".
The Australian Federal Police said the warrant was in relation to "allegations of publishing classified material" and that it "relates to a referral received on 11 July 2017 from the Chief of the Defence Force and the then-Acting Secretary for Defence".
The Afghan Files were published by the ABC on 10 July 2017.
The police said Tuesday's and Wednesday's raids were not connected, adding: "Both however relate to separate allegations of publishing classified material, contrary to provisions of the Crimes Act 1914, which is an extremely serious matter that has the potential to undermine Australia's national security."
It defended its actions, saying they had "been independent and impartial at all times".
ABC journalist John Lyons, who live-tweeted the raid, said that police were going through 9,214 documents found on the ABC systems one-by-one, including "thousands of internal ABC emails". ■