Mehol Sadain, who heads the National Commission on Muslim Filipinos, said Sunday he had written to Pilar College in the mixed Muslim-Christian port city of Zamboanga to demand it reverse its policy.
While the school was right to claim it could exercise academic freedom, Sadain said it should do so with “justice and fair play”.
“Pilar College should realize that while educational institutions can formulate their own policies, the same should not run counter to existing laws and state policies,” Sadain said.
The complaint has reached the local city council, which asked the school to reply to the allegations.
The school is believed to be the first in the Philippines to enforce an outright ban on wearing the hijab.
Sadain noted that an education department policy states that Muslim girls should be allowed to wear their head coverings in school and be exempted from non-Muslim religious rites.
But the school, run by the Congregation of the Religious of the Virgin Mary, said in its letter to the council that it could not “deviate” from its Catholic leanings.
It said students from other religions were welcome to enrol but must strictly follow its non-hijab policy.
“Rules and regulations are explained to them, particularly the non-wearing of the hijab or veil,” the school said.
“This is part of academic freedom in connection with which the school has the right to choose whom to teach,” it said.
It was not clear what percentage of students were Muslim but it is fairly common that children from different denominations or religions mix at school in the mainly Catholic but largely tolerant Philippines.
Education department officials in Manila were not available for comment Sunday.
More than 80 percent of the Philippines’ nearly 100 million population are Catholic, while Muslims form a large minority in the south of the country.