The deportation saga of Australian missionary nun Sister Patricia Fox in the Philippines has taken a new twist with at least a further delay to her being forced out of the country.

The Bureau of Immigration has accepted an administrative payment allowing consideration of a requested extension of her missionary visa that expires at midnight on Wednesday after 27 years.

Since being arrested and detained for 22 hours in mid-April, the 72-year-old Catholic nun has defied the odds through legal actions and appeals – often near the final hour – to stop authorities from putting her on a flight back to Australia.

She told AAP on Wednesday that, in the latest development, processing of the application for an extension of her missionary visa could take up to 60 days.

“I think they could well do it faster than that,” she said.

In any event, she had been advised that, even if this bid is rejected, she would still be given a 30-day tourist visa.

President Rodrigo Duterte has accused Sister Fox of unwarranted involvement in partisan political protests. Photo: Getty

Efforts to remove the Australian from the Philippines were spurred by President Rodrigo Duterte accusing her of unwarranted involvement in partisan political protests.

Sister Fox has over many years joined protest rallies calling for the release of people deemed to be political prisoners, as well as campaigns supporting poor farmers and indigenous people.

She and her legal team have argued that she has a right to freedom of expression the same as anybody else, including other missionaries and foreigners in general.

Sister Fox has been refused a personal dialogue with Justice Secretary Menardo Guevarra, who has been acting President of the Philippines while Duterte is travelling overseas, on the grounds that it would be improper.

Mr Guevarra has previously ruled in her favour and against the Bureau of Immigration at key junctures.

“It looks like my case is going to continue for a while yet,” she said.

-AAP