In a damning report Tuesday, United Nations special rapporteur Michel Forst said several human rights defenders had refused to meet him because of the fear of persecution.
"Many activists spoke of an atmosphere of fear, censorship and retaliation," Forst said.
Forst has just finished a two-week tour of Australia on behalf of the UN's Human Rights Council to assess how well human rights defenders were being treated in the country.
In a statement, the Australian government said the special rapporteur "has not presented a balanced view of the situation of human rights defenders in Australia."
But Australian Human Rights Commission President Professor Gillian Triggs told CNN Forst's statement had been accurate and accused Australia's government of having a "ideological objection" to advocacy.
'Need for change'
Forst told CNN he had been shocked by the state of human rights in Australia after his tour of the country.
"I came with the idea that there would be a safe and enabling environment (for human rights defenders)," he said. "That is not the case. There are some practices that need to be changed."
As part of 14 recommendations for the Australian government, Forst called for inquiries into government intimidation of the Human Rights Commission, impartial investigations into violence against human rights defenders and revoking laws which restrict the right to protest freely.
His warnings come as yet another damning report into Australia's offshore detention policy
accused the government of torture, abuse and turning the tiny island of Nauru into an "open-air prison."
Australian Prime Minister Malcolm Turnbull rejected Amnesty International's claims as "absolutely false."
Hundreds of refugees and asylum seekers have been detained by Australia in centers in Nauru and Papua New Guinea, and strict controls have been placed on reporting from the camps.
'Extraordinary lengths' to gag whistleblowers
Forst highlighted what he described as the "extraordinary lengths" Canberra has gone to in stopping whistleblowers, public servants and contractors sharing information about human rights abuses.
He pointed to the November 2015 arrest of a Doctors for Refugees convenor on a plane for "disobeying a flight attendant," which Forst said may have been politically motivated.
Numerous whistleblowers "validated the stories of service providers whose contracts were canceled for speaking out in broad terms about what they witnessed," he added.
"Other contractors, such as Save the Children, have been subjected to raids and egregious allegations of misconduct, removed from operations and had their personal and professional reputations targeted by politicians and media."
Under the Border Force Act, anyone who makes "unauthorized disclosures"
about Australia's detention camps can be imprisoned for up to two years.
During his discussions with the government, Forst said he was reassured that no prosecution had been brought yet under the Act. Still, he urged the government to urgently review it.
Attacks on human rights leaders
Forst called for an inquiry into government attempts to "intimidate" and harass the Australian Human Rights Commission and its president, Gillian Triggs.
Former Prime Minister Tony Abbott's government repeatedly attacked Triggs
after she released a report into abuse of children in offshore detention centers.
Abbott blasted the report as "biased," while Immigration Minister Peter Dutton
and Attorney General George Brandis called on Triggs to resign.
Saying he was "astounded" by the attacks on rights defenders by senior government officials, Forst called for full funding to be restored to the Commission, which had its budget cut under Abbott's government.
Speaking to CNN, Triggs said it was "enormously encouraging" to hear Forst's conclusions. "For him to identify this as a matter of significance was of course important to the Commission's staff and me personally," she said.
"There's an ideological objection by this government ... that entities should not be advocating. It's essentially a violation of the right to freedom of speech and it has impacts on so many areas of the law."
Right to protest under threat
Multiple additional issues were raised by the UN report, including state laws restricting the right to peaceful assembly and the protection of the legal rights of indigenous Australians.
Laws are currently being proposed in Western Australia to limit citizens' ability to protest, based on Tasmania's 2014 Protection from Protesters Act.
Forst warned Canberra that such laws contravene Australia's obligations under international human rights law.
"Freedom of peaceful assembly is an essential part of democratic societies," he said in his statement. "Demonstrations and protests help raise awareness about human rights and encourage dialogue."