An army spokesman confirmed the attack, which took place in Ituri province on Tuesday evening, and blamed it on the Allied Democratic Forces (ADF), a Ugandan militia active in eastern Congo since the 1990s, which has pledged allegiance to the Islamic State.
The army killed five fighters and rescued a five-year-old girl who had been kidnapped, spokesman Antony Mwalushayi said. He did not give a civilian death toll.
Gilbert Sivamwenda, president of the local human rights group for the chiefdom of Babila Babombi, said there were 16 dead in Biakato including 14 civilians and two ADF fighters.
About 15 farmers were also missing and several other people who cannot be found and are not responding to calls, Sivamwenda said.
"The nature of the attack was terrifying. They looted my shop before taking five members of my family into the bush," said Biakato resident Augustin Kyala Malembe, who also counted 16 dead and said dozens of people were kidnapped.
"The army intervened but the damage was done."
The ADF stages frequent deadly raids on villages in eastern Congo despite joint operations by the Congolese and Ugandan armies to stamp it out. The group killed about 40 civilians in five villages in a string of attacks between Thursday and Monday.