Philippine President Rodrigo Duterte says he personally ordered an investigation into a 71-year-old Australian nun with a view to deporting her for "disorderly conduct" and being an "undesirable alien".

Key points: Rodrigo Duterte says Patricia Fox's conduct is a "violation of sovereignty"

Rodrigo Duterte says Patricia Fox's conduct is a "violation of sovereignty" President appears determined to have nun deported

President appears determined to have nun deported Sister Fox denies involvement in partisan politics

Patricia Fox, the mother superior at a Catholic order in Manila's Quezon City, was detained on Monday by Philippine Bureau of Immigration officials and questioned over her involvement in recent human rights actions in Mindanao.

"You are a foreigner! Who are you? No, it's a violation of sovereignty," he declared while speaking about Sister Fox at a military ceremony in Manila.

The President suggested Sister Fox should save her criticisms for Australia's refugee policy.

"We never did that to Australia. We never did that to a European country," Mr Duterte said.

"Why don't you criticise your own Government, the way you handle the refugees, hungry and dying and you turn them back to the open sea?"

Sister Fox was released on Tuesday after her arrest provoked protests at the Bureau of Immigration office where she was held, including a visit from Manila's auxiliary bishop and complaints from senior Catholic Church figures.

Sister Patricia Fox has been involved with human rights missions in the Philippines. ( Twitter: Pamalakaya Pilipinas )

A presidential spokesman said that her arrest was an error. But Mr Duterte said there was no mistake.

"It was not the military who arrested the nun, the Catholic nun from Australia," he said.

"It was upon my orders implemented by the Bureau of Immigration and I take full responsibility legal or otherwise for this incident.

"I ordered her to be investigated. Not deported at once. Not arrested but invite her to an investigation for disorderly conduct.

"The Philippine laws provide that I can deport you, or refuse you entry, if you are an undesirable alien."

I decide who enters the Philippines, Duterte says

Philippines President Rodrigo Duterte has faced widespread criticism for human rights violations. ( AP: Wong Maye-e )

He then launched into an extraordinary, emotional attack on the nun.

"Freedom of expression is unlimited and it goes for everybody but to otherwise undermine and treat the Philippines like a mattress to wipe your feet on, that is something else," Mr Duterte said.

"Who are you? No it's a violation of sovereignty."

Sister Fox had been hopeful that she would be allowed to stay in the Philippines.

But during his comments on Tuesday Mr Duterte appeared determined that the nun should leave.

"The order of who gets in and who gets out is with me. Not in Congress. Not in the Supreme Court," he said.

"You do not try to criticise her [the Philippines]. You can come and enjoy the sites.

"But do not insult us every time that you open your mouth, with your foot inside."

Nun denies involvement in partisan politics

A "tired" Sister Fox, who was a human rights lawyer in Melbourne before she moved to the Philippines 27 years ago, said she hadn't attacked the Philippines or attended any partisan political rallies.

Sorry, this video has expired Sister Pat defends her involvement in activism after being detained in the Philippines

She said Bureau of Immigration investigators showed photographs of herself at two recent events in Mindanao during a "fact finding" mission to the island, which remains under martial law.

"They showed me two photos — one of which was myself meeting political prisoners with a group," she told the ABC.

"The other one I think it was workers from Coca Cola who had been put off after eight years, so that was all they showed me, so I said, they're not rallies.

"They said that I took part in political rallies forbidden by foreigners. Nothing I've taken part in has been partisan political.

"I've certainly joined the workers in their call for ending contractualisation, the farmers for land, the tribal people for their indigenous rights, but they're not partisan politics.

"It's all consistent with the social teachings of the Church and part of our mission."

Australia's Department of Foreign Affairs said it was providing consular assistance to Sister Fox.

It is the second time that Mr Duterte has made controversial comments about an Australian woman.

During the campaign before the 2016 general election he made extremely offensive comments about Australian lay minister Jacqueline Hammil, who was raped and murdered in Davao City in 1989.

Mr Duterte said he wished he had been first in line to rape her.

Mr Duterte claimed that he had been joking and then attacked Australia's ambassador to the Philippines, Amanda Gorely, who said that rape and murder should never be joked about.