The Bureau of Immigration order issued on Thursday also called for the inclusion of Sister Patricia Anne Fox in the agency's blacklist which would prohibit her from returning to the country.
Australian nun Patricia Fox has once again been ordered to leave the Philippines.
Ms Fox, who has been living in the Philippines since 1990, drew the President's wrath after joining a fact-finding mission in April to investigate alleged abuses against farmers - including killings and evictions by soldiers fighting guerrillas.
In June, the Department of Justice granted Fox an appeal, which reinstated her missionary visa and allowed her to stay in the country while deportation proceedings continued, PNA reported.
It said Fox violated the terms of her missionary visa.
The Bureau of Immigration's order cites evidence of Fox urging the release of political prisoners and actively supporting labor groups.
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"I'm disappointed but that's the order and we will look at what we can do about it", she said.
President Rodrigo Duterte admitted that he was behind the BI probe into Fox's "disorderly conduct".
Fox's lawyers said they were utterly dismayed and would appeal to fight "this kind of persecution".
The immigration bureau, however, said that allowing Fox to join political rallies and other such activities would allow other aliens to do so as well.
Mr Duterte, 73, has also launched a deadly crackdown on drugs and has railed against human rights critics, especially foreigners whom he accuses of meddling in his nation's affairs.
His administration barred a critical Italian politician, Giacomo Filibeck, from entering the Philippines in April.