"I said the raid, in its very public form and in the sweeping nature of the information sought, was clearly designed to intimidate," she said in her first public statement since the unprecedented raids.
"It is impossible to ignore the seismic nature of this week's events: raids on two separate media outfits on consecutive days is a blunt signal of adverse consequences for news organisations who make life uncomfortable for policymakers and regulators by shining lights in dark corners and holding the powerful to account."
The former magazine editor asked the minister to rule out future police action against journalists, but he refused.
"Mr Fletcher declined to provide such assurances while noting the “substantial concern” registered by the Corporation."
The AFP hasn't ruled out laying charges following the back-to-back raids this week.
Search warrants were executed at the ABC's Ultimo headquarters over 2017 stories on allegations Australian soldiers may have carried out unlawful killings in Afghanistan, based on leaked Defence papers.
The warrant executed on Annika Smethurst's home was over the 2018 publication of a leaked plan to allow the Australian Signals Directorate to spy on Australians.
The raids have sparked debate about press freedom and calls from media advocates for new laws to protect journalists and whistleblowers.
Prime Minister Scott Morrison and Home Affairs Minister Peter Dutton have repeatedly denied the government had any involvement in the investigation or the timing of the search warrants.
Ms Buttrose said the onus should always be on the public's right to know and if that wasn't reflected in current laws, they should change.
"In my view, legitimate journalistic endeavours that expose flawed decision-making or matters that policymakers and public servants would simply prefer were secret should not automatically and conveniently be classed as issues of national security," she said.
"As ABC chair, I will fight any attempts to muzzle the national broadcaster or interfere with its obligations to the Australian public.
"Independence is not exercised by degrees. It is absolute."
Additional reporting by AAP