Sister Patricia Fox, 71, has been accused of illegally engaging in political activism as the government cracks down on foreign critics on its soil.
“We find Fox Patricia Anne, Australian national, in violation of the limitations and conditions of (the Philippines immigration law) and order her deportation to Australia,” said the government order.
Duterte has supported Fox’s removal.
He ordered her arrest in April and previously said he wanted her investigated for “disorderly conduct”.
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.
She is accused of taking part in news conferences, labour-related fact-finding missions and protests calling for political prisoners to be freed, for human rights and land rights to be respected and for martial law to be lifted on the southern island of Mindanao.
Last month her deportation was halted when Justice Secretary Menardo Guevarra said immigration authorities used the wrong procedure to expel her.
The decision gave Fox a reprieve but Guevarra also ordered the immigration authorities to hear a case on her visa’s cancellation along with pending deportation proceedings.
The new order issued yesterday would also bar her from re-entering the Philippines.
The immigration office spokeswoman did not return calls for comment.
Fox’s lawyers said they plan to appeal within the next few days.
“Under the (immigration service) rules, if we file the order is not executory. And we will file an appeal,” lawyer Jobert Pahilga said.
“Very sad, but hopefully I can challenge it still,” the nun separately said in a text message.
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.
“Don’t let her in because that nun has a shameless mouth,” Duterte said in April, accusing the Sisters of Our Lady of Sion missionary of “disorderly conduct”.
Fox has denied engaging in politics, saying her actions were part of her work to advocate for justice and peace.