MANILA—The Australian missionary whom President Rodrigo Duterte ordered investigated for supposed "disorderly conduct" has left the Philippines, her home for nearly three decades, after her temporary visitor visa expired on Saturday.

Patricia Fox, the 72-year-old missionary kicked out of the country over alleged "political activities," left Manila onboard Philippine Airlines flight 209 bound for Melbourne at about 9:40 p.m.

She flew pending her appeal to the deportation order against her before the Department of Justice.

• Before leaving PH, Australian missionary Fox urges Duterte to listen to poor

Before leaving the country, Fox attended a thanksgiving Mass at the St. Joseph’s College in Quezon City. Some of her supporters also held a caravan as they accompanied the nun on her way to the Ninoy Aquino International Airport.

The Bureau of Immigration earlier ordered Fox's deportation for supposedly violating the terms of her missionary visa by allegedly joining "partisan political activities" after she took part in a human rights fact-finding mission in the country's troubled south.

The church worker was initially detained last April 16 and was released "for further investigation" the next day. The Immigration bureau also claimed Fox took part in protest actions by farmers' groups, also an offense against her visa.

The nun has repeatedly denied taking part in "partisan political activities," insisting that her missionary work involves dealing with farmers, indigenous peoples, and victims of social injustice—people commonly helped by Left-leaning organizations.

• Sister Fox leaving PH, insists she has done nothing wrong
• Fox denies joining 'political activities', says she's doing church work

Duterte himself admitted that he ordered the investigation of Fox for alleged "disorderly conduct" but denied that he sought her arrest and deportation. He also accused the missionary of having a "foul mouth."

• Duterte rejects call to allow Aussie nun’s stay in PH

"Hanggang ngayon hindi ko alam kung bakit si Digong ayaw sa akin," Fox, who is fluent in Tagalog, laughingly told her supporters after the Mass.

(Until now, I don't know why Digong does not like me.)

Asked for her message to Duterte, she said: "Sana makikinig siya ng mga daing ng mga maliliit na tao, hindi lamang military, hindi lamang mga businessman, pero mga urban poor, mga magsasaka mga manggagawa, mga katutubo."

(I hope he listens to the plight of the poor, not just the military or businessmen, but also the urban poor, farmers, workers, and the indigenous people.)

Despite Fox's departure, her lawyer Jobert Pahilga said the fight against her deportation case, which he believes would set a precedent for other missionaries like her, would continue.

"If the Department of Justice will eventually reverse and set aside the decision of the Bureau of Immigration, her name will be erased from the blacklist [of] tourists and she can go back here and maybe apply for [a] missionary visa," he said.

— With reports from Henry Atuelan, ABS-CBN News and Raoul Esperas