Police were following a car believed to be carrying supporters of Habib Rizieq Shihab on a highway, just after midnight on Sunday, when the shootout began.
Police chief Fadil Imran said six followers of Shihab were killed in the confrontation.
Jakarta has accused Razieq – head of the Islamic Defender’s Front (FPI) – of violating health protocols during the coronavirus pandemic, after he returned last month to the country from Saudi Arabia.
He went into self-exile in April 2017, following two lawsuits against him.
When he landed in Jakarta, tens of thousands of people flocked to the airport to celebrate his return, despite the pandemic restrictions.
Before he left Indonesia, Rizieq, led a large movement against Jakarta’s former Christian governor, Basuki Tjahaja Purnama – known as Ahok – who was accused of insulting Islamic sanctities.
In May 2017, Ahok was sentenced to two years in prison for blasphemy in the world’s biggest Muslim majority country.
The rallies, led by Razieq back then, were the biggest since the fall of Indonesia’s former ruler Suharto in 1998.
Since his return, the cleric has announced plans to embark on a “moral crusade” and has met some politicians and opposition figures.