The deaths occurred on Sunday in the Beni region of North Kivu province.
Suspected Ugandan Islamist rebels killed three civilians in eastern Democratic Republic of Congo, despite an offensive by government troops, sources said on Monday.
The deaths occurred on Sunday in the Beni region of North Kivu province, where government forces launched a campaign against the Allied Democratic Forces (ADF) militia on January 13.
"There was an incursion by the ADF yesterday (Sunday) in Kokola. Three people — a motorcycle taxi driver and his two customers — were killed before the army intervened," the administrator of Beni district, Bernard Amisi Kalonda, told AFP.
The incident was confirmed by Jonas Mbusa, a community leader.
The army's spokesman in the region, Captain Mak Hazukay, told AFP that that the ADF "incursion yesterday at Kokola was repelled. Operations are continuing." He gave no further details.
Present in DR Congo since 1995, the ADF was initially created by Muslim radicals to oppose Ugandan President Yoweri Museveni's rule.
Today, they are a number of armed groups that hold swathes of territory in eastern DR Congo, battling for control of mineral resources.
Congolese authorities and the UN mission in DR Congo, Monusco accuse the ADF of having killed more than 700 civilians as well as combatants in the Beni region from 2014-16.
The ADF is also accused of killing 14 UN peacekeepers in eastern DR Congo on December 7, in the biggest single loss of peacekeepers in nearly a quarter of a century.
The government last week declared it was waging "war" on the ADF and a Congolese militia, the Yakutumba, which is active in South Kivu province, several hundred kilometres (miles) to the south.
However, troop losses have been heavy. Diplomatic sources say 22 troops were killed on Friday in an ADF attack.