Sister Patricia Fox’s renewable missionary visa, which was due to expire in September 2018, was cancelled on Monday.
She has been labelled an “undesirable” foreigner for what the country’s Bureau of Immigration says is “her involvement in partisan political activities.”
The 71-year-old Australian nun has 30 days to leave the Philippines.
An immigration spokeswoman said she can still return as a tourist, but not as a missionary.
In a one-page order, immigration bureau head Jaime Morente asked Fox to leave the Philippines after “she was found to have engaged in activities that are not allowed under the terms and conditions of her visa.”
Fox said in a statement that she was surprised by the order and that she hoped authorities would change their minds before the 30 days were up.
She told Australia’s ABC TV: “For me, it is part of my mission as a Catholic sister to stand beside those whose human rights have been violated, who are asking for help.”
“We will file a motion for reconsideration on this order,” said Jobert Pahilga, Fox’s lawyer. “She has not participated in any partisan activity. She is a nun.”
The left-wing activist group Bayan (Nation) condemned the expulsion order of a nun who “has done so much for Philippine farmers in her nearly three decades stay here.”
“The Duterte regime is paranoid and afraid of an elderly nun working for human rights and social justice for the poor,” Bayan leader Renato Reyes said in a statement.
“The deportation order of Sister Pat is indeed despicable and utterly shameful,” said Mr Reyes.
Last week in a speech to soldiers, Philippines President Duterte said he ordered the immigration bureau to look into Sister Patricia’s political activities in the country.
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