"As of Wednesday night, we recovered the bodies of 40 people" after their boats capsized, Jean Bakatoye, vice governor of South Ubangi province, told AFP.
"The toll is still provisional as other bodies were swept downstream," he said.
The civilians were trying to cross the Ubangi River, which marks part of the border with the neighbouring Republic of Congo.
They were trying to escape fighting involving DR Congo troops and "outlaws," Bakatoye said.
The events took place in the remote border area of Dongo, after an army position came under attack on Sunday, he said.
"Several soldiers" were injured, he said, although four witnesses told AFP they had seen the bodies of two troops and four assailants.
On Monday, army reinforcements arrived, prompting villagers to panic, fearing a wider conflict, Bakatoye said.
The Dongo region was shaken by a revolt by the Enyele ethnic group in 2009, which was put down by the Congolese army the following year.
Fighting left an estimated 270 dead and displaced 200,000 people.
Sub-Saharan Africa's biggest country, the DR Congo is struggling with local conflicts, and in remote areas the control of the central government in Kinshasa is weak.
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