Sister Patricia Fox, who spent nearly three decades working with Philippine laborers, farmers and urban poor, was accused of illegally engaging in political activism as Duterte's government cracked down on foreign critics on its soil.
"I hope (Duterte) listens to the voice of the little people, not just the military, not just the businessmen, but the farmers, the workers, the tribal folk", she said in a pre-departure press conference.
Australian nun Sister Patricia Fox hugs supporters in the Philippines before boarding a plane to Melbourne.
The government barred Italian politician Giacomo Filibeck, who has criticised the anti-drug crackdown, from entering the Philippines in April.
Fox said she came to Duterte's attention after going on a fact-finding mission in the president's home province of Mindanao.
Although she fought the deportation, her passport was officially confiscated by the Philippines government on Wednesday and she was forced to leave.
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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.
Australian nun and human rights campaigner Patricia Fox says she has mixed feelings about returning to Australia after being deported from the Philippines.
Sister Patricia Fox was met with a hero's welcome as she walked through the arrival hall at Melbourne Airport on Sunday, swamped by a chanting crowd, banners and flashing cameras.
"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.
When Fox was in Manila, she was working with the families of the victims who were killed in the drug war, which has left thousands dead.
"I know a lot of mothers, wives who have lost someone", Fox said.
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She also thanked members from the Filipino community who were there to welcome her.
After her missionary visa was cancelled and she was put on a blacklist, the nun was given a temporary visa that expired on November 3.
"They should look start looking at Australian companies, particularly mining companies, because they're hiring goons and ... you know we have to start being responsible for what's happening over there", she said.
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.
Members of the Phillipines Australia Solidarity Association were also at the airport to welcome the nun home and praised her courage and unwavering fight for justice.
"The law is clear- The entry and admission of an alien is a matter of privilege, and not a right", Bureau of Immigration spokeswoman Dana Sandoval said on Saturday.
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