Michelle Guthrie has resigned just two-and-a-half years into her five-year term as the ABC's managing director, effective immediately.
Appointed to the role in May 2016, Guthrie was the ABC's first female managing director.
"This decision has been driven by our commitment to deliver the best possible outcomes for our loyal audiences and the best possible experience for our own people".
Guthrie has yet to comment on this morning's decision. "We are very grateful for all her hard work".
"The ABC board has legislated independence in relation to management appointments and the Government respects the duty and role of the board in these matters".
"The board wishes to thank Michelle for her contribution to the ABC", Mr Milne said.
"By law, Managing Directors are selected by the ABC Board independently of the Government and Opposition of the day", the ABC noted in its statement.
Guthrie, who was only about halfway through her contract, has been under fire from critics outside the organisation and within it.
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Milne and Guthrie reportedly had a frosty relationship, clashing over how to deal with a hostile government in Canberra.
Anderson will serve as acting managing director while Guthrie's permanent replacement is found. Anderson is now Director, Entertainment & Specialist and has worked in the media industry for more than 30 years.
News Corp has been unrelenting in its attacks on the ABC, accusing it of political bias and pushing back at the competition it presents to commercial operators.
Mr Anderson is the director, entertainment & specialist responsible for broadcast, television networks, radio music networks, podcasts and specialist radio content.
Succession planning receives continuous attention from the ABC Board.
Ms Guthrie, a former Foxtel and Google executive and media lawyer, has been a controversial figure at the ABC as she managed tighter budgets along with leading expansion into new business areas.
The board was at pains to assert that, by law, the process of hiring a Managing Director is one done exclusively by the board, totally independent of the Government and the Opposition of the day.