The shooting occurred in the village of Nyakova on the banks of Lake Albert in Congo's eastern Ituri province.
"The soldier opened fire on all those around him. A dozen people died," Ituri army spokesman Jules Ngongo said via telephone.
Search teams are looking for the soldier, a member of Congo's navy, and an investigation into the incident has been opened, he said.
Village chief Oscar Baraka Muguwa said 13 people were killed, including nine children, Reuters reported.
It was unclear what led the soldier to begin shooting. According to Muguwa, the soldier was concerned his child would be buried without him there.
MP/PR