People in white Islamic robes packed out a massive park in the capital, chanting Islamic verses and singing the national anthem, with over 20,000 security forces deployed to prevent a repeat of violence that erupted at the last protest against Basuki Tjahaja Purnama.
Purnama, known by his nickname Ahok, is being prosecuted for allegedly committing blasphemy over comments he made about the Koran during an election campaign, which have sparked widespread anger in the world's most populous Muslim-majority country.
The decision to prosecute Purnama, Jakarta's first non-Muslim governor for half a century, has not been enough to quell anger and conservative groups are now demanding his arrest. Protesters waved banners that read "jail Ahok" as they marched en masse through the city's streets in the early hours to converge on the park.
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National police chief Tito Karnavian was shouted down when he went up on stage in the park, with the crowd pumping their fists in the air and yelling "jail Ahok", who is also a member of Indonesia's small ethnic Chinese minority.
Jakarta police spokesman Raden Prabowo Argo Yuwono estimated at least 100,000 protesters had converged on the park by mid-morning and said so far the rally was peaceful.
It was peaceful during the day but descended into violence as night fell, with Muslim hardliners hurling missiles at security forces and setting fire to police cars.
Security forces responded with tear gas and water cannon, in clashes that left one person dead and hundreds injured.