Between 3,000 and 4,000 people are at the peacekeeping base at Kitchanga in North Kivu province in an early test for a UN-brokered peace accord aimed at ending two decades of war and strife in the mineral-rich region.
Clashes between the DR Congo army and the Alliance of Patriots for a Free and Sovereign Congo, better known under its French acronym APCLS, erupted in the region on Wednesday.
UN deputy spokesman Eduardo del Buey said the toll from the fighting had risen to at least 36 dead. One peacekeeper from the UN force, MONUSCO, has also been wounded.
"This morning MONUSCO reported gunshots in the area. The mission says that between 3,000 and 4,000 Congolese have now taken refuge around its base in Kitchanga," the spokesman said.
"MONUSCO is closely monitoring the area, including with its combat helicopter," del Buey said.
A UN peacekeeping spokesman told AFP that 10 civilians, six government soldiers and 20 militia fighters had been killed so far.
The APCLS is a longstanding militia in the region which made its name battling the late dictator Sese Seko Mobutu in the 1990s when widespread wars in DR Congo and neighboring countries left millions dead.
Kitchanga is in the Masisi region of North Kivu, close to where the army and UN peacekeepers are in a showdown with the M23 group. Deadly fighting has also been reported this week between M23 factions.
The unrest involving M23 and the APCLS comes after a UN-brokered peace deal signed on Sunday by 11 African nations, including DR Congo.
DR Congo's President Joseph Kabila vowed to step up efforts to extend government control to the lawless eastern part of his country. The other nations have in turn promised not to interfere in the affairs of neighbors.
UN experts have accused Rwanda and Uganda of backing the M23 fighters. Both countries deny the charge and signed the non-interference pledge.
But UN Secretary General Ban Ki-moon said in a report released Wednesday that foreign countries are still backing rebels in DR Congo and must face "tangible consequences" for their actions.