The rise in such practices has affected teachers too. Henny Supolo, head of Yayasan Cahaya Guru, a teachers’ nonprofit foundation, said that from 2007 to 2010, the organization provided training to 4,500 teachers from 2,000 schools, an overwhelming majority of whom were female teachers from public schools. “We noticed that almost all of them wore jilbab as uniform,” Ms. Supolo said, referring to what Indonesians call the Islamic head scarf. “Jilbab has become part of uniform for female public school teachers whom we met.”

This is alarming, she said: “If jilbab has become part of the uniform at public schools, then the function of public schools as a place to sow plurality to our children will disappear.”

Retno Listyarti, secretary general of the Indonesian Teachers’ Union Federation, put the issue bluntly: “Public schools have become religious schools,” she said.

Some schools now hold a daily mass recital of the Koran before formal classes begin. In one school in eastern Jakarta, Muslim students spend 15 to 20 minutes reading the Koran every morning, guided through a public address system, said a teacher at the school, speaking on condition that neither she nor the school be identified, for fear of professional repercussions.

Christian students sit together in one room, within hearing of the Koranic recital, to read the Bible, the teacher said. Hindu and Buddhist students, who don’t have their own religious teachers in the school, read their religious texts while sitting in the same rooms as their Muslim classmates reciting the Koran.

“This shows that the majority is always right, while the minority has to adapt,” the teacher said.

Indonesia, which has the world’s largest Muslim population — more than 200 million, or nearly 90 percent of its citizens profess the Islamic faith — is often praised as a model of moderate Islam.

But in recent years, the country has faced a rise of Sunni radicalism and religious intolerance. The Indonesian Children Protection Commission has warned that radical tenets are being increasingly being taught at every age level, from kindergarten to university.