The selection of Dr Johns, according to representatives of the sector, is "bizarre" and forms part of a wider effort to clamp down on criticism of government policy and the public advocacy work of charities, which the incoming commissioner has previously targeted.
But Assistant Minister to the Treasurer Michael Sukkar has rejected the concerns, saying Dr Johns will merely apply the law as an "independent regulator" and downplaying the contentious views he has expressed about activism and broader social issues.
Dr Johns, who was an MP in the 1980s and 1990s and a minister in the Keating government, has criticised how registered charities lobby for their causes and receive government funding. He has also said poor women who have children - singling out those who are Aboriginal - are "cash cows" and argued people who rely on welfare payment should be forced to use contraception.
A former senior fellow at conservative think-tank the Institute of Public Affairs, Dr Johns has also been a critic of environmental groups who campaign against fossil fuels and charities who send money overseas and "give aid to Third World kleptomaniacs".
The appointment has shocked Community Council of Australia CEO David Crosbie, who said it was "bizarre" as Dr Johns was a campaigner against charities.
"It's a continuation, for us, of a theme that says the government wants to silence the voice of charities," Mr Crosbie said.
"Gary Johns has made numerous public statements that clearly indicate he is opposed to many charities and their work. Only a government committed to attacking the charities sector would put someone like Gary Johns in as head of the ACNC."
Mr Crosbie also said the writer and former MP was not qualified to lead 100 staff, administer complex laws and regulations, reduce red tape in the sector and build the community's trust and confidence in charities.
Responding to the concerns, Dr Johns said he would be "neither friend nor foe".
"My job is to apply the law and advocacy is a charitable purpose when taken in conjunction with other charitable purposes," Dr Johns said.
Mr Sukkar added: "I don't think we ever should require that we expunge views or comments that have been over a 30 or 40 year career. But as Dr Johns has pointed out, he is here to apply the law as it is contained in the [Charities Act] and the fact that he has a deep understanding of these issues in a more philosophical sense is a strength."
The government says his appointment is the result of a merit-based process that involved a selection panel drawn from the public service.
But Mark Purcell, CEO of the Australian Council for International Development, which represents NGOs in the aid sector, expressed concern that the government would now be looking to change the law in an upcoming review, empowering Dr Johns to launch a crackdown.
"We're concerned that the government's game plan is to have to the charity regulator tie up charitable critics of government policy between now and the next election," Mr Purcell said.
Earlier this week, the government also unveiled new donations laws that will ban foreign contributions to charities for social and environmental advocacy deemed to be political.
Mr Purcell said the appointment and foreign donations ban looked like efforts in "Putin's Russia and Modhi's India" to silence critics.
Labor charities and not-for-profits spokesman Andrew Leigh said the appointment was "like putting Ned Kelly in charge of bank security".
"Mr Johns has been a foe of charities and he has been one of the strongest critics of charities in Australia. He has attacked Indigenous charities, he has attacked mental health charities and he has attacked charities that attempt to engage in advocacy," Dr Leigh said.