Ahmed Mushaddeq leads the new Al Qiyadah Al Islamiyah sect.
He handed himself into Jakarta police after threats against his followers were made by Muslim hardliners.
The sect has been described as deviant and blasphemous by the country’s powerful Muslim organisation, the Indonesian Ulema Council because it promotes an alternative view of Islam.
Mushaddeq has also raised the ire of Muslims after claiming to be the next prophet to follow Mohammed.
That statement has led to violence, with some of his supporters physically harassed.
Experts warn that kind of intimidation could escalate as more radical sects continue to surface across the archipelago.
Professor Azyumardi Azra, President of Indonesia’s State Islamic University spoke to Radio Australia’s Asia Pacific program about the case.
“Their sect claims to be originally come from Islam but they introduced a very different kind of teachings of Islam. In fact they do not recognise the prophecy of Mohammed for instance, so that creates problems,” he said.
The group says it does not believe in the five pillars of Islam, (praying five times a day, compulsory contributions to charity and for the pilgrimage to Mecca as well as the obligation to fast) and Ahmed Mushaddeq has declared that he is the new prophet.
Professor Azra says the police estimate 30,000 to 40,000 people across the country, mostly young university students, unemployed young people, belong to the sect.
He says uncertainty about the future makes the sect attractive to young people.
“I think because of the social and cultural crisis now in Indonesia, because we are not really settled yet because of the big changes not only in politics but also in other field of life, in terms of social and cultural life. In our social life we have a lot of problems. We have a good number of unemployed people and also we have a problem of the future of students,” he said.