A demand from ABC chairman Justin Milne that a journalist be fired because the government hated her will be the subject of a departmental inquiry.
ABC chairman Justin Milne's demand that a journalist be sacked is under investigation, but the public broadcaster's board is standing by him.
Staff on Wednesday unanimously voted for Mr Milne to step down while a departmental investigation takes place, but the board has confidence in him to continue in his job.
An explosive email has revealed Mr Milne told former ABC managing director Michelle Guthrie to fire chief economics correspondent Emma Alberici in May.
"They [the government] hate her," he wrote in an email to Ms Guthrie obtained by Fairfax Media.
"We are tarred with her brush. I think it's simple. Get rid of her. We need to save the ABC - not Emma. There is no guarantee they [the coalition] will lose the next election."
There are also reports Mr Milne complained about two other journalists who upset the government, political reporter Andrew Probyn and radio broadcaster Jon Faine, as well as several controversial programming choices.
Mr Milne is also said to have tried to stop Triple J's Hottest 100 song countdown being moved from Australia Day.
Former ABC journalist and board member Matt Peacock told the broadcaster on Wednesday the chairman said words to the effect: "Malcolm will go ballistic if we do that".
But it's understood in the ABC board phone hookup on Wednesday afternoon members said they had confidence in Mr Milne and reaffirmed Monday's decision to sack Ms Guthrie.
Ms Guthrie was sacked after Mr Milne said her relationship with the government could have been better.
Communications Minister Mitch Fifield announced his department secretary will run an inquiry into the matter and report as soon as possible.
"It is important for the community to have confidence in the independence of the ABC," he said in a statement.
Senator Fifield had earlier said he was not aware of any member of government involving themselves in ABC staff matters.
The board will cooperate with the inquiry.
Labor leader Bill Shorten said the government had made Mr Milne's job "untenable".
"No political party has the right to interfere like this with the ABC," Mr Shorten said.
Prime Minister Scott Morrison, who was consulted over the inquiry, earlier tried to side-step the controversy.
"I think it would be very unfair and premature for me to be offering opinions about things that are yet to be established," he told reporters in Sydney.
Former ABC managing director David Hill says Mr Milne "has no choice" but to step down given the circumstances.
"It's sad, but I think the chairman, Milne, really has to really consider his position and consider resigning," he told the ABC.
Two of Ms Alberici's stories on corporate tax earlier this year were re-written following complaints from the government.
Mr Milne issued a statement without directly responding to the reported email.
"The job of the ABC board is to independently govern the corporation, protect its best interests, ensure that it is well funded, well managed, and that our content is of the highest standards," he said.
"That is precisely what the board has done and will continue to do."