"We have made a strategic and tactical withdrawal from Rumangabo, in consultation with our partners, to better prepare the next steps together," the U.N. mission, known as MONUSCO, said in a post on Twitter.
It did not provide further details.
The loss of the major military base is a setback for Congo and a further blow to the security outlook in the conflict-hit east. The crisis has also deepened a standoff with neighboring Rwanda over its alleged support for the rebels, which it denies.
U.N. troops have been supporting DRC forces in the fight against the M23, which launched a new offensive in October and seized the town of Kiwanja last Saturday, breaking months of relative calm.
"Its fall is another humiliation for Kinshasa. But it also raises serious questions, once again, of how an extremely small rebellion can do this on their own," said Jason Stearns, founder of the Congo Studies Group, a research institute at New York University.
Kenya deployed troops on Wednesday to the Democratic Republic of Congo to battle a rebel offensive in the country's troubled east in a joint operation by a regional bloc, President William Ruto announced.
"As neighbors, the destiny of DRC is intertwined with ours," Ruto said at a ceremony in Nairobi, adding that the troops -- part of a regional force that includes soldiers from Burundi, Uganda and South Sudan -- were "on a mission to protect humanity."
Goma, the capital of Congo's North-Kivu province, has been effectively cut off from the upper half of the province since the capture of Kiwanja. More than 90,000 people have fled their homes since fighting resumed on Oct. 20, according to the U.N.
In August, U.N. experts said they had found solid evidence Rwanda had been interfering militarily in eastern Congo. Rwanda's government has disputed the findings.
The spat between Kinshasa and Kigali has led to recalled ambassadors.
The escalation prompted East African heads of state to hold a joint call on Tuesday and schedule a meeting of their defense chiefs to address the security crisis, the office of Burundi's president said in a statement.