Muslims constitute a majority in most regions of Java, Sumatra, West Nusa Tenggara, Sulawesi, coastal areas of Kalimantan, and North Maluku. Muslims form distinct minorities in Papua, Bali, East Nusa Tenggara, parts of North Sumatra, most inland areas of Kalimantan, and North Sulawesi. Together, these non-muslim areas originally constitute more than one third of Indonesia prior to the massive transmigration effort sponsored by the Suharto government and recent spontaneous internal migration.

Internal migration has altered the demographic makeup of the country over the past 3 decades. It has increased the percentage of Muslims in predominantly Christian eastern parts of the country. By the early 1990s, Christians became a minority for the first time in some areas of the Moluccas. While government-sponsored transmigration from heavily populated Java and Madura to less populated areas contributed to the increase in the Muslim population in the resettlement areas, no evidence suggests that the Government intended to create a Muslim majority in Christian areas, and most Muslim migration seemed spontaneous. Regardless of its intent, the economic and political consequences of the transmigration policy contributed to religious conflicts in Maluku, Central Sulawesi, and to a lesser extent in Papua.