Anglicare Australia, the St Vincent De Paul Society, Baptist Care and UnitingCare have called for the government to drop the proposed legislation, saying it would make it harder to advocate for their missions, and increase the regulatory burden.

The new powers for the Charities and Not For Profit Commissioner were developed in response to animal welfare groups registered as non-for-profits that trespassed on farms as part of their activism, with the responsible minister Michael Sukkar saying the changes were aimed at political activists "masquerading as charities".

Other corners of the charities and not-for-profit sector have already voiced opposition to the changes, but the four major faith-based organisations decided to speak up in fear of how subjective and wide-ranging the powers would be.

"We could be targeted if our staff or volunteers commit minor offences. We could be held responsible for how other people use our materials," said chair of Anglicare Australia Rt Rev Dr Chris Jones.

"We could even be shut down if the commissioner thinks it's 'more likely than not' that we'll do something wrong."

Under current legislation, charities must not engage in conduct, or omit to engage in conduct that be dealt with as an indictable offence or attract a fine of over $13,320. The proposed changes would expand that rule to include summary offences in all states and territories, meaning a charity could be deregistered if a protest it takes part in blocks traffic for example. It also extends to the actions of individual members, and the way material produced by a charity is used by people or groups unrelated to the charity.

The breadth of the changes has raised alarm in the sector, including a section of the explanatory statement with the exposure draft which said the rules could be enforced "if the ACNC commissioner reasonably believes that it is more likely than not that the entity will not comply with a governance standard".

"This means it is not necessary for a registered entity to be charged or found guilty of a relevant summary offence for the ACNC commissioner to take appropriate enforcement action," the explanatory statement from the government said.

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Executive director of Baptist Care Australia Nicole Hornsby said the changes would limit the ability of charities to undertake legitimate and lawful advocacy.

"The breadth of their application to include such subjective measures as a 'belief' that they 'may' commit a minor offence is totally unreasonable," Ms Hornsby said.

The charities and Labor have pointed out the powers that would be handed to the commissioner go well above powers that exist for businesses.

"Rules like these would be unthinkable for businesses, but they are the latest in a long line of attacks on charities," said Dr Jones.

"We're calling on the government to abandon these changes and support us in our work - helping Australians in need."

Labor's spokesman on issues related to charities and the not for profits sector Andrew Leigh said the proposed rules were "a bridge too far".

"If a charity is breaking the law or encouraging people to break the law it already can be deregistered but it doesn't get deregistered for thought crime, the anticipation that it might cause a summary offence to happen," Dr Leigh said.

Businesses would be outraged if ASIC were to be given similar powers, Dr Leigh said.

"This is just another part of the government's war on charities. It will just mean they have less freedom to advocate in the public space," Dr Leigh said.

Charities were "rightly terrified" of Charities Commissioner Gary Johns having such powers, Dr Leigh said. A Labor minister in the Keating government, Dr Johns was a controversial pick for the role by the Turnbull government. He has written in opinion columns that contraception should be made mandatory for welfare recipients and called Indigenous women on welfare "cash cows".

Assistant Treasurer Michael Sukkar is responsible for the charities and not-for-profit sector, and for the bill, which is due in parliament in coming months. He did not respond when contacted for a response.

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