MANILA - An Australian nun who has angered President Rodrigo Duterte for joining anti-government rallies left the Philippines on Saturday (Nov 3), following a long battle against her deportation.

The nun, Sister Patricia Fox, 71, boarded a plane at 9.15pm that took her to Melbourne, her home town.

Shortly after landing in Melbourne, she told reporters: "At present, (in the) the Philippines, the human rights abuses are just increasing, and it is a reign of tyranny at present."

"There has been a culture of impunity for a long time, and it is getting worse," she said.

Hours before she left, Ms Fox offered unsolicited advice to Mr Duterte: "Listen to the poor, not just the military. Listen to the urban poor, farmers, workers, indigenous people. Listen to them, and act on their behalf, not just the wealthy's."

The reed-thin missionary had been in the Philippines advocating for the poorest for nearly 30 years.

Since April, she had been battling repeated attempts by immigration officials to deport her. Her missionary visa, though, expired while various appeals were still being pursued. She was instead given a temporary tourist visa that expired on Saturday.

Before she went to the airport, Ms Fox attended an emotional mass to say farewell to hundreds of her supporters who protested her expulsion and vowed to work for her return, possibly after Mr Duterte steps down in 2022.

Ms Fox herself held out hope she would one day return to the Philippines.

"There will come a time I will return one day," she said.

The leftist group Bagong Alyansang Makabayan (New People's Alliance) called her departure a "great injustice".

On the eve of her departure, Ms Fox urged Filipinos in a statement "not to succumb to fear and inaction".

She insisted that her actions while in the Philippines were "neither political nor partisan, but part and parcel of my apostolate and missionary work".

"In contrast, sitting idly, keeping one's silence, doing nothing when injustice and oppression is happening… is repugnant to the social doctrines and teachings of the church for salvation and liberation to the poor and powerless," she said.

Mr Duterte's spokesman Salvador Panelo said in a text message on Saturday that Ms Fox's expulsion "is a timely reminder to all foreigners who stay or sojourn in this country that they are not entitled to all the rights and privileges granted to the citizens of the Philippines, including the absolute exercise of political rights inherently exclusive to Filipino citizens".

He said Ms Fox, in participating in rallies, fact-finding missions and news conferences, "violated the conditions of her stay, thereby mocking our laws and abusing the hospitality extended to her by the host country".

Mr Duterte had accused Ms Fox of "disorderly conduct" after she joined a fact-finding mission in April to investigate alleged abuses against farmers in the president's home town of Davao.

She went to see farmers detained on charges of possessing explosives, and attended a news conference by workers who were fired after demanding better wages and conditions.

Shortly after that, she was arrested briefly on charges of violating her visa's terms.

Ms Fox's battle to stay in the Philippines has put a spotlight on the wider issue of foreigners' involvement in human rights campaigning.

Mr Duterte has been sensitive to criticisms, especially by foreigners, who he says have no right to meddle in his country's domestic affairs and criticise his bloody crackdown on the narcotics trade that has left thousands of suspects dead.

The government barred Italian politician Giacomo Filibeck, who has criticised the anti-drug crackdown, from entering the Philippines in April.

Four months later, Australian rights activist Gill Boehringer, was barred entry for having attended a protest in 2015, allegedly in violation of immigration laws.

Also this year, three foreign missionaries, including an American, were detained and deported in July after visiting the southern Philippines to investigate allegations that the army had carried out abuses there, including the December killings of at least eight members of an indigenous community in the province of Lake Sebu.

Ms Fox landed in the Philippines in 1990 as a member of the Sisters of Our Lady of Sion, a congregation of nuns founded in France in 1847 and famed for harbouring Jews fleeing from Nazi persecution in World War II.

A former practising lawyer who worked with indigent clients in Australia, Ms Fox has said she has been educating landless Filipino farm hands and factory workers about their rights.