The deportation saga in the Philippines of Sister Patricia Fox is to come to an end on Saturday after the long-serving Australian missionary and critic of president Rodrigo Duterte had her passport confiscated.

The 72-year-old has been in the Philippines for 27 years but will fly to Australia on Saturday after a battle that has put a spotlight on the wider issue of expatriate involvement in human rights’ campaigning.

The nation’s hard-line president, Rodrigo Duterte, who is accused of sanctioning thousands of extra-judicial killings, accused Fox of partisan political involvement. “You don’t have the right to criticise us,” Duterte said earlier this year.

Fox and supporters counter that all foreigners, including missionaries, have an inalienable right, enshrined by the country’s constitution, to challenge abuses.

Human Rights Watch has noted that Fox’s case highlights a dangerous climate of impunity.

But it also served as a warning to other foreign nationals not to speak out against the country’s catastrophic human rights violations, said Carlos Conde, a researcher with the rights’ organisation.

“What happened to Sister Fox should be viewed in the context of Duterte’s systematic attempt to frustrate accountability for the killings by targeting critics from politics, civil society and the media; threatening them and imprisoning them,” Conde said.

Since April, Fox has clung on in the Philippines despite repeated attempts by immigration officials to get rid of her.

But her missionary visa expired while various appeals were still being pursued and she was instead given a temporary tourist visa that expires on Saturday.

Her ordeal has stirred debate in the Philippines about the wider issue of whether expatriates should be free to take a stand on human rights concerns.

Australians, including members of various church and non-government organisations, have found themselves in trouble for speaking their minds in the Asia-Pacific region.

And Australian journalists have been imprisoned, detained, harassed or banned in countries such as Indonesia, Vietnam, China, Thailand, Myanmar, Malaysia, Nauru and Papua New Guinea.

Recently, Australian filmmaker James Ricketson was released on a royal pardon after having been imprisoned in Cambodia as a result of his local political activism and criticism of entrenched prime minister Hun Sen.

Australian journalist Alan Morrison, who ran a news website in Thailand’s tourist hub of Phuket, was prosecuted in 2014 for criminal defamation after highlighting rights violations against Rohingya refugees from Myanmar. He was eventually acquitted.

And on 8 August this year, Australian lawyer Gill Boehringer, 84, was detained at the main international airport of the Philippines capital, Manila, and held there until 14 August when he was sent back to Australia.

The Bureau of Immigration said he had been blacklisted for prior involvement in an anti-government rally and for meeting with leftist insurgents. The latter claim was strongly refuted by Fox.

Fox was part of an international fact-finding mission this year into extra-judicial killings on the southern island of Mindanao, where Duterte was previously a long-serving mayor.

The inquiry documented 54 cases of killings, torture and illegal detentions as well as harassment and intimidation.

And there have been up to 20,000 extra-judicial killings as part of a so-called anti-drug war unleashed by Duterte.

Immigration officials collected a dossier on Fox that includes photos of her at protest rallies, including one of her holding a placard calling for the release of “political prisoners”.

Fox said anyone challenging rights’ abuses was being branded as a sympathiser of armed leftist militants of the New People’s Army (NPA).

She was to attend a special Catholic mass for her in Manila and was also scheduled to hold a media conference on her treatment.

Supporters in a convoy of colourful vehicles planned to accompany her to the international airport on Saturday where she had been told intelligence agents would escort her on to a Melbourne-bound flight.