An Australian nun has been ordered to leave the Philippines because of her alleged involvement in activities against the country's government.

Patricia Fox, 71, has lived in the Philippines for 27 years.

Philippines President Rodrigo Duterte last week accused her of disorderly conduct and called her an undesirable alien.

Immigration Authorities in Manila have recommended her missionary visa be cancelled, and given her 30 days to leave the country.

The deportation order accuses Sister Patricia of openly and actively participating in activities such as rallies, press conferences and fact-finding missions which supposedly violated the terms and conditions of her missionary visa.

Sorry, this video has expired 'Criticise your own government': Duterte lashes out at Australian nun

Her lawyer Jobert Pahilga said the order did not specifically accuse her of engaging in anti-government activities.

He argued that it showed Sister Patricia had not violated the terms of her visa, but that her activities were consistent with her missionary work of promoting peace, social justice and human rights.

Mr Pahilga said her work was much desired by the people she served, including farmers, indigenous people, workers, the poor and marginalised.

He called on the Philippines government to respect her rights to continue her missionary work.

Sister Patricia Fox says she is simply helping people assert their rights ( ABC News: Phil Hemingway )

The order gives her 10 days to lodge an appeal and prove that she is not an undesirable alien.

Sister Patricia is a coordinator of a Philippine congregation of Roman Catholic nuns called Notre Dame de Sion.