An Australian Catholic nun has been given 30 days to leave the Philippines after infuriating President Rodrigo Duterte by attending protest rallies.

Patricia Anne Fox, a 71 year-old superior of the Notre Dame de Sion in the Philippines, a congregation of Catholic nuns, was detained for a day last week after Mr Duterte ordered her investigation for “disorderly conduct”.

Immigration bureau head Jaime Morente said on Wednesday he had revoked her missionary visa because “she was found to have engaged in activities that are not allowed under the terms and conditions of her visa”.

Sister Pat, who has been in the country for more than 27 years, has 30 days to exit the Philippines after receipt of the order.

Her renewable missionary visa, which was due to expire in September 2018, was cancelled on Monday, but an immigration spokeswoman said she can still return to the mainly Catholic south-east Asian country as a tourist, not as a missionary.

Earlier this week, Sister Pat said she would be “very sad” to leave behind her missionary work.

“When they come out and support you, they make you want to be here,” she told the ABC.

“So many messages. Overwhelming. I don’t want to leave here.”

Mr Duterte’s threats were “frightening”, she admitted.

He’s clearly angry. That’s frightening. He has the power to say I have to go tomorrow.”

A lawyer for the Australian nun, Jobert Pahilga, said she would appeal.

“We will file a motion for reconsideration on this order,” Mr Pahilga told AAP. “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.”

In a speech last week to soldiers, Mr Duterte said he ordered the immigration department to look into Sister Pat’s political activities in the country.

“It’s a violation of sovereignty,” Mr Duterte said, accusing the nun of badmouthing his administration.

“You do not have that right to criticise us. Do not insult my country.”

His spokesman, Harry Roque, even showed journalists photos of Sister Fox speaking at farmer and labourer protest rallies in Mr Duterte’s hometown in southern Davao City early this month.

-with AAP