The riots on Sunday were one of the worst outbreaks of violence since a peace pact in February 2002 ended three years of sectarian battles - that killed about 5000 people - in parts of the Maluku islands.
"The victims are 98 in total, 10 of whom are dead," Moluccas provincial police chief Brigadier-General Bambang Sutrisno told reporters.
Separate reports from hospital staff and a local Muslim official confirmed five people, including a high school girl, were shot dead and one person died of a heart attack.
Witnesses said street battles raged throughout Sunday afternoon near the former governor's office.
They said the UN mission which houses several agencies, and several cars parked there, were set on fire.
Trouble began after the mainly Christian pro-independence Front for Maluku's Sovereignty staged a street convoy, carrying separatist flags to mark the 54th anniversary of the movement.
They traded jeers, insults and stones with mainly Muslim opponents of the separatist movement.
Paramilitary police and soldiers tried to disperse the crowd, but were pelted with stones.
Ambonese set fire to the UN
mission during the anniversary
El Shinta radio said police also arrested about 20 separatist supporters who were trying to mark the anniversary of the founding of the self-proclaimed South Maluku Republic (SMR).
The SMR was proclaimed in 1950, a year after the Dutch formally granted Indonesia independence, by mostly Christian residents loyal to colonial rule.
A local journalist said Muslims, fearing further violence, had fled their homes in the Waringin area that borders the mainly Christian area of Batugantung.
He said men carrying machetes, spears and other weapons could be seen on the streets.
In January, courts in Ambon sentenced at least 12 separatists to between 30 months and 15 years in prison for treason after they were caught hoisting the separatist flag on 25 April last year.
The movement was quickly quelled and is not now believed to have widespread support among Christians in Maluku.
But the government, which faces more serious separatist unrest in Aceh and Papua, is cracking down on any independence moves.