The emphasis on the Pancasila in public schools has been resisted by some of the Muslim majority. A distinct but vocal minority of these Muslims prefer to receive their schooling in a pesantren or residential learning center. Usually in rural areas and under the direction of a Muslim scholar, pesantren are attended by young people seeking a detailed understanding of the Quran, the Arabic language, the sharia, and Muslim traditions and history. Students could enter and leave the pesantren any time of the year, and the studies were not organized as a progression of courses leading to graduation. Although not all pesantren were equally orthodox, most were and the chief aim was to produce good Muslims.

In order for students to adapt to life in the modern, secular nation-state, the Muslim-dominated Department of Religious Affairs advocated the spread of a newer variety of Muslim school, the madrasa. In the early 1990s, these schools integrated religious subjects from the pesantren with secular subjects from the Western-style public education system. The less-than 15 percent of the school-age population who attended either type of Islamic schools did so because of the perceived higher quality instruction. However, among Islamic schools, a madrasa was ranked lower than a pesantren. Despite the widespread perception in the West of resurgent Islamic orthodoxy in Muslim countries, the 1980s saw little overall increase in the role of religion in school curricula in Indonesia.

In general, Indonesia's educational system still faced a shortage of resources in the 1990s. The shortage of staffing in Indonesia's schools was no longer as acute as in the 1950s, but serious difficulties remained, particularly in the areas of teacher salaries, teacher certification, and finding qualified personnel. Providing textbooks and other school equipment throughout the farflung archipelago continued to be a significant problem as well.

Data as of November 1992