The leading journalists' union in the country said the two raids represented a "disturbing pattern of assaults on Australian press freedom".
Video from Sydney Morning Herald Journalist Lucy Cormack shows the moment AFP officers arrived at the ABC headquarters.
The Afghan Files were published by the ABC on 10 July 2017.
Ms Smethurst's home was raided over the 2018 publication of a leaked plan to allow the ASD to spy on Australians.
Ms Buttrose, who is only the second woman to lead the ABC board, said an "untrammelled" media which upholds the community's right to information has driven her journalistic career for nearly five decades.
"Public interest is best served by the ABC doing its job, asking hard questions and dealing with genuine whistle-blowers who risk their livelihoods and reputations to bring matters of grave import to the surface".
Six police officers entered the corporation's offices in Sydney with a warrant naming three senior journalists and executives involved in a two-year-old investigative report.
"This warrant relates to the alleged publishing of information classified as an official secret, which is an extremely serious matter that has the potential to undermine Australia's national security", police said in a statement.
The ABC Chair made these remarks after meeting with the Minister for Communications, Cyber Safety and the Arts, Paul Fletcher on Thursday, in which she asked him for assurances that the broadcaster would not be subject to similar raids in the future, which he refused to provide.
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Yesterday Police raided the Canberra home of Australian journalist Annika Smethurst, looking for the source of a leak of confidential information.
"They are about more than hunting down whistle blowers that reveal what governments are secretly doing in our name, but also preventing the media from shining a light on the actions of government".
"There are also clear rules protecting Australia's national security and everybody should operate in accordance with all of those laws passed by our parliament". These laws seek to muzzle the media and criminalise legitimate journalism.
"Honest and committed to telling the truth in the Australian public's interests".
"Australia believes strongly in the freedom of the press and we have clear rules and protections for the freedom of the press", the leader told Australian the media from the United Kingdom, where he is taking part in the commemoration of the D-day landings in Normandy. Suddenly, just days after a federal election, the Federal Police launches this attack on press freedom.
Innes Willox - a former political adviser, diplomat and now chief executive of the Australian Industry Group - said he was anxious about the perceived politicisation of supposedly independent government departments and agencies.
"MEAA demands to know who is responsible for ordering these coordinated raids, and why now".
"For years the Liberal and Labor parties have engaged in a high-stakes game of bluff which has seen the introduction of anti-democratic laws in the guise of national security legislation".