The Cooperative for the Development of the Congo, CODECO, group, one of many militias operating in the conflict-ridden east, was behind the attack, said Djugu territory administrator Ruphin Mapela and civil society leader Dieudonne Lossa.
"The victims were praying to the Lord, but unfortunately militiamen identified as CODECO opened fire on them," Lossa said.
Both said that 9 civilians, 4 assailants and a soldier were killed.
Mapela said that militants attacked Mesa, Cepac and Aumopro churches located near the shore of Lake Albert in the Bahema-Nord chiefdom.
"We call on the population to remain calm as the armed forces pursue these criminals to put them out of action," Ituri army spokesman Jules Ngongo Tshikudi said.
CODECO claims to defend the interests of Lendu farmers, who have long been in conflict with Hema herders.
The CODECO raids have worsened a longstanding humanitarian crisis in Ituri province, where some 3 million people are in desperate need of aid, according to a United Nations humanitarian agency.