Dozens of congregations, gathering nearly 3,000 believers mainly in rural areas, have formed over the years outside of the official structure. Some pursue radical interpretations of Islam not traditional among the nearly 2 million Bosnian Muslims.
Such illegal groups are seen as hotbeds of Islamic radicalism and some members have joined the Islamic State group in Syria.
The Islamic Community on Friday urged members of such groups to abandon self-proclaimed imams who are luring people into a "monstrous" ideology. Last month they sent envoys to the congregations urging people to switch to an official congregation.