The Duterte administration has taken similar action against a number of foreign critics of the president’s policies. In August, the immigration bureau detained an 84-year-old Australian professor, Gill Boehringer, at the Manila airport and barred him from entering the country because he had joined protests against Mr. Duterte.

Also this year, three foreign missionaries, including an American, were detained and deported in July after visiting the southern Philippines to investigate allegations that the army had carried out abuses there, including the December killings of at least eight members of an indigenous community in the province of Lake Sebu.

One of Sister Fox’s lawyers, Katherine Panguban, said they would continue to appeal her case to the immigration bureau while the nun is in her native Melbourne. “This clearly shows that this government is intolerant of dissent,” Ms. Panguban said of the case.

A spokesman for Mr. Duterte, Salvador Panelo, said on Saturday: “The departure of Sister Patricia Fox is a timely reminder to all foreigners who stay or sojourn in this country that they are not entitled to all the rights and privileges granted to the citizens of the Philippines.”

“She underwent a legal process where she was given the opportunity to be heard,” he said, adding, “We wish Sister Fox well in her travel, and we thank her for whatever good deeds she has performed during her stay in the country.”

Officials in the Catholic Church, which has considerable influence in the Philippines and has been active in the opposition to Mr. Duterte, said Sister Fox’s expulsion was a “blow to the missionary spirit” of the church.

“The government should have taken the moral high ground in taking up the case of the embattled nun,” said Father Jerome Secillano of the Catholic Bishops Conference of the Philippines.