Snipers and bombers killed one civilian and injured 11 earlier on Wednesday, said Al-Fatah hospital chief Rivai Ambon.
But violence appeared confined to areas south of the centre and daily life slowly started to resume elsewhere in the eastern city in the Maluku islands.
A national police spokesman said 36 people, including two policemen hit by snipers, had been killed since a banned parade by Christian separatists sparked off bloodshed on Sunday. He said 159 people had been injured.
The violence was the worst since a pact in February 2002 ended three years of sectarian fighting in which some 5,000 people died.
At least 200 homes and many other buildings including the United Nations mission were set ablaze. The UN has temporarily withdrawn some staff.
The UN mission was set ablaze
SCTV television said about 100 empty houses were torched on Wednesday in the Batugantung and Waringin areas southeast of Tanah Lapang Kecil.
More than 2,000 Muslims and Christians have fled their homes, according to a crisis centre operated by a Muslim student body. They said about 500 Muslims had taken refuge at an entertainment park and at the Al-Fatah mosque.
Those who stayed in their homes remained confined to their respective sectors behind hastily-improvised street barricades.
In the Tanah Lapang Kecil and Waringin districts, scene of most of the recent clashes, residents installed three shipping containers taken from the port to provide shelters from snipers in exposed spots.
Sporadic gunshots could still be heard from the area in the afternoon. Locals said these apparently were warning shots fired to keep groups from other religions and police and troops at bay.
Despite the danger of snipers, curious onlookers still gathered on street corners.
The Jakarta government has rushed 400 extra paramilitary police and 450 more troops to the waterfront city, which is still scarred by battles in previous years.
"...Witnesses had seen members of the TNI (armed forces) involved in the torching (Tuesday) of the Nazareth church in Batu Merah"
provincial government, Maluku
Politicians in Jakarta and Christian clergymen and others in Ambon have faulted local police for failing to crack down on Sunday's parade, which was seen as provocative to Muslims.
During the 1999-2002 conflict some troop and police units were accused of bias either towards Muslims or Christians.
A provincial government spokeswoman said more than 1,000 Christians protested on Wednesday at police headquarters to demand that troop reinforcements from outside Ambon be withdrawn.
"They say witnesses had seen members of the TNI (armed forces) involved in the torching (Tuesday) of the Nazareth church in Batu Merah," the spokeswoman said.
Indonesia's population is 87% Muslim but Christians and Muslims live in roughly equal numbers in the Malukus.
In Jakarta the hardline Indonesian Mujahidin Council, which advocates Islamic law, called for Indonesians to fight separatism in the Malukus and elsewhere.