ABC's investigations editor John Lyons tweeted a photo of the search warrant which showed the targets included two ABC journalists, the organisation's news director and a former Australian military lawyer, David William McBride, who was charged past year with leaking national secrets.
David Anderson, the ABC's managing director, said in a statement that "it is highly unusual for the national broadcaster to be raided in this way".
Australia is a "world leader" in passing anti-terror and national security laws that threaten media freedom, he said.
"This is a serious development and raises legitimate concerns over freedom of the press and proper public scrutiny of national security and defence matters", Anderson said.
During yesterday's raids, John Lyons, an ABC journalist, tweeted from within the office, revealing the search warrant allowed the AFP to "add, copy, delete or alter" material on the ABC's computers.
This morning, AFP raided ABC's Sydney headquarters. There is one common thread - they make the government look bad - granting new powers to a spy agency, a lapse in border patrol and a criminal culture within our armed forces.
"What we're seeing here is no-one in the government being prepared to defend the role that media has in our democracy, which is essential", he said.
Asked about the raid after an event commemorating the 75th anniversary of D-Day in Britain, Australian Prime Minister Scott Morrison told reporters that he had no prior knowledge of the AFP operation.
The AFP reportedly spent nine hours searching through more than 9,000 ABC emails and documents.
Police raided the home of a News Corp editor a day earlier, although they said the raids were unrelated.
"The AFP is a strong supporter of press freedom", he said on Thursday. "That's inevitable. There are plenty of stories I can think of that the government might be targeting next".
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".
CBC News was instrumental in pushing the Federal Government to toughen the laws preserving the confidentiality of journalistic sources.
"We stand by Annika and we will not resile from our campaign to protect the public's right to know about important decisions governments are making that can and will impact ordinary Australian citizens", Michael Miller, News Corp Australasia executive chairman, said in a statement. But what happens when things go wrong?
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