Charities Minister Zed Seselja said he had "serious concerns" that activist organisation Aussie Farms could undermine public trust in established charities like the St Vincent de Paul Society and has referred Aussie Farms to Charities Commissioner Gary Johns who has the power to strip non government organisations of their special tax status.

"I support charities advocating for causes they believe in but when groups are promoting unlawful activity, they are stepping over the line," Senator Seselja said.

"Charities like Vinnies [the St Vincent de Paul Society] and the Salvos [Salvation Army] and many others do amazing work selflessly caring for those in need. It is offensive they are given the same legal status as groups inciting criminal activity."

Charitable status is offered to not-for-profit groups, including religious organisations, homeless shelters, disability service groups, universities, animal welfare groups and artistic groups.

The tax classification allows registered organisations to qualify for tax concessions, including allowing donors to claim their contributions as tax-deductible gifts.

The Morrison government has already moved to bring Aussie Farms under the Privacy Act, exposing the organisation to major fines.

Last week, it passed anti-farm trespass laws through the House of Representatives.

Aussie Farms' Chris Delforce said activists would not be deterred by the threat.

"Both Scott [Morrison] and Zed need a reminder that they are supposed to be governing for all Australians, not just big agribusiness," he said.

"Perhaps instead of going after charities and whistleblowers, they could criminalise animal cruelty and start assisting animal farmers in moving towards more ethical and environmentally sustainable methods of income."

The organisation has promised to continue its campaign against factory farming which includes the publication of an online map of every farm and abattoir in Australia, raiding slaughter houses across the country. It brought Melbourne's CBD to a halt in May this year with a sit-in demonstration.

Earlier this year, activist James Warden entered a pig farm in the middle of the night and live-streamed conditions on social media.

During another protest in Harvey, Western Australia, shots were fired by farmer Jason Parravinci who says he was scaring off vermin in an incident just after an altercation with Warden and other activists.

Warden is expected to face trial in Western Australia charged with two counts of aggravated burglary, two counts of stealing and three counts of trespass over separate incidents. He has pleaded to all three counts of trespass and not guilty to the others.

Labor's charities spokesman Andrew Leigh said, "Australian laws already provide strict limits around the activities of charities. If the Morrison Government has sensible proposals for reform, we will consider them. But given the Coalition's six-year war on charities, we need to be sure this isn't just more scare-mongering from a government that has tried repeatedly to make life harder for charities".