Christian officials said nine of their faith were killed. Islamic officials said three Muslims died. Both sides said most victims were shot by soldiers.
More than 30 people were hospitalized with gunshot wounds. Others were cut by swords or hit by rocks, homemade spears or arrows.
The violence flared late Wednesday on an island already devastated by months of communal fighting, and residents said security forces continued to fire shots Thursday.
"We heard shots before dawn. Two neighbors were wounded by gunfire. Another was stabbed," said resident Una Noya in a telephone interview.
Fierce fighting among rival religious groups first erupted in Ambon Jan. 19.
Since then, violence has spread to five neighboring islands and has left more than 200 people dead in Maluku province. Thousands of homes, shops and other buildings have already been damaged or burned.
Thousands of troop reinforcements have been deployed, but they have failed to quell the violence, despite orders to shoot troublemakers.
The latest killings in the main city, also named Ambon, triggered a new series of protests by Muslims in other parts of Islam-dominated Indonesia. There are fears that religious strife might spread.
Both Muslims and Christians accused the military of shooting unarmed civilians during the latest mayhem.
"At least two of the dead were shot in their homes by soldiers," said Semiwaile Runi, a Protestant church official.
Jusuf Ely, an official at an Ambon mosque, said two Muslims were shot and killed and one was burned to death in his house.
Dozens of houses were set on fire in the city, 1,400 miles east of Jakarta, when clashes among rival gangs erupted in six places around the city, police said.
About 90% of Indonesia's 210 million people are Muslim, making it the world's most populous Islamic nation. However, parts of Maluku, known in Dutch colonial times as the Spice Islands, have large Christian populations.
The religious clashes continue as Indonesia grapples with rising political and social tensions fueled by its worst economic crisis in 30 years.
In Jakarta, Muslim students called on the government and military to take stronger action to stop the violence.
And on Sulawesi Island near Ambon, thousands of Islamic students marched through the streets of Ujung Pandang city Thursday and warned of the possibility of retaliation against the Christian minority there.
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