Charities and non-government organisations have expressed alarm at the Turnbull government's appointment of controversial former Labor MP Gary Johns as the head of the Australian Charities and Not-for-profits Commission.

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.

Commissioner of the Australian Charities and Not-for-profits Commission Dr Gary Johns and Assistant Minister to the Treasurer Michael Sukkar at a press conference at Parliament House. Credit:AAP

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.