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Outgoing CBA President Justin Milne said no government member ever asked him to fire journalists because they did not like the broadcaster's coverage.
He says he resigned Thursday because the controversy around him was putting pressure on the national broadcaster.
The head of the communications department is investigating reports that Milne has asked former director Michelle Guthrie to sack journalists of Emma Alberici and Andrew Probyn because the government did not like their articles.
The ABC Board of Directors met Thursday morning without Mr. Milne and asked him to withdraw during the investigation.
"I said" well, I think in fact, I should resign because it's clear that there's a lot of pressure on the organization, "said Milne on Thursday. 39; ABC.
"It's clearly not a good thing that everyone is trying to do their job with this kind of fire storm, so I wanted to provide a relief valve."
An email showed that Mr Milne had asked Ms Guthrie – who had been fired on Monday – to dismiss Ms Alberici in May.
"They (the government) hate it," he wrote in an email to Ms. Guthrie from Fairfax Media.
Milne also allegedly ordered Ms. Guthrie to dismiss Mr. Probyn, saying "just shoot him" because Mr. Turnbull hated the journalist.
"No one from the government has ever sounded and told me what to do with respect to the ABC," said Mr. Milne.
"Nobody ever told me to hire anyone, send anyone away or do anything else – they absolutely did not do it."
Mr. Turnbull says that he did not ask that specific journalists be deported.
"This is not correct.In the end, I have never called anyone to be fired," said the former prime minister to reporters in New York.
"I am worried about the accuracy and impartiality of the reports."
The council meets again on Thursday to decide who will be acting chair.
"The board and the president made the right choice," said Premier Scott Morrison.
"It is time for the ABC to resume a normal transmission, both independently and without bias, which is what Australian taxpayers pay and deserve."
Communications Minister Mitch Fifield ordered his departmental secretary, Mike Mrdak, to investigate and report within days.
Labor Party leader Bill Shorten said Milne's position was untenable after he "let himself be intimidated" by the government.
"More worrying for the nation, is how the Liberal Party seeks to interfere with the independence of the ABC, to reduce its funding and to seek to sell it," tweeted Mr. Shorten after resignation.
Green Senator Sarah Hanson-Young called for a complete review of ABC's board of directors to give the broadcaster a "fresh start".
ABC leaders will appear before a Senate forecast committee in October.
