By Agence France-Presse
Sister Patricia Fox, 71, who was briefly detained last week, will be the second foreigner who has spoken out recently against Duterte's policies to be expelled, as the government hits back at critics of his human rights record.
The immigration service said it had cancelled the visa of Fox, who relocated to the Philippines in 1990 as a member of the missionary Sisters of Our Lady of Sion.
"We direct Fox to leave the Philippines within 30 days from receipt of this order," it said in a statement, adding that the nun had "engaged in activities that are not allowed under the terms and conditions of her visa".
Fox said in a statement Wednesday she helped to train Filipino farmers and tribesmen in organic farming to improve their incomes, as well as "to advocate with them for their rights to land, livelihood, peace, justice and security".
"It seems this is what has brought me into conflict with the Philippine government," she added. "I am still hoping for a chance to explain how I see my mission as a religious sister and maybe the decision can be reconsidered."
'You insult me'
Her lawyer Jobert Pahilga said the deportation order violated the nun's right to due process, and she would appeal to have the immigration service ruling rescinded.
The immigration bureau held the nun overnight last week but released her without charges.
Following her detention, Fox said she had recently joined a fact-finding mission to investigate alleged human rights abuses against farmers by soldiers fighting communist rebels.
Hours after her release, Duterte announced he had personally ordered her arrest as a warning to foreigners to stop criticising his government.
"I ordered her to be investigated... for disorderly conduct," Duterte said in a speech last week.
"You insult me under the cloak of being a Catholic priest, and you are a foreigner! Who are you? It is a violation of sovereignty," Duterte said, apparently referring to Fox.
Duterte has previously launched verbal attacks against critics of his government's narcotics crackdown, which has killed thousands of alleged dealers and users.
The International Criminal Court's chief prosecutor launched a preliminary investigation in February into allegations of extrajudicial killings.
This prompted Duterte to withdraw from the ICC and threaten to arrest the chief prosecutor if she travels to the Philippines.
Earlier this month Manila also deported Italian Giacomo Filibeck, deputy secretary general of the Party of European Socialists, who had previously condemned "extra-judicial killings" in Duterte's anti-drug war.