Maluku provincial chief, Brigadier General Bambang Sutrisno, confirmed the toll on Monday, adding that hundreds of extra troops and paramilitaries were being rushed to the city.
Several buildings, including the UN mission, a large hotel and a church, have all been set on fire.
Fires hit at least five residential areas, including the two refugee resettlement areas of Airmata Cina and Tawake.
About 400 paramilitary police are scheduled to arrive in addition to one battalion from the military "to guard all critical areas".
Muslim and Christian residents, some armed with machetes and sticks, stood guard in their respective areas though recent reports suggest a reduction in violence.
Cause of riot
Trouble began after the mainly Christian pro-independence South Maluku Republic (SMR) staged a street convoy, carrying separatist flags to mark the 54th anniversary of the movement on Sunday.
The SMR was proclaimed in 1950, a year after the Dutch formally granted Indonesia independence, by mostly Christian residents loyal to colonial rule.
More than 400 anti-riot police are
expected to end the violence
Many had hoped for an end to Christian-Muslim violence after a peace pact in February 2002.
Nearly 5000 people died and half a million were forced to flee their homes in the three years prior to the truce.
Maluku military spokesman Major Paiman said the army's three existing battalions in Ambon had been put on alert. He gave no total but a battalion can range from between 600 and 900 men.
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 now is not 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.