Congo invited the Rwandan army to help confront FDLR rebels last month, in a sign of improved relations between the two countries after a 15-year period in which they fought two wars.
Some FDLR rebels took part in Rwanda's 1994 genocide and then fled to Congo, sparking years of violence as Rwanda's powerful Tutsi-led army then invaded its mineral-rich neighbour.
Rwanda said it invaded Congo during the 1990s to hunt the Hutu force, but it did not defeat them and, in the process, Rwanda was accused of plundering Congo's resources and backing other Congolese rebels.
The UN peacekeeping force in the DRC, the world's biggest, said the pullout could spark reprisals against civilians and let Rwandan rebels retake ground they lost during the joint offensive.
"The FDLR have a very ugly past, but we haven't seen this level of violence in years."
Anneke Van Woudenberg
Human Rights Watch
Earlier in the month, the US-based Human Rights Watch (HRW) said Rwandan rebels had killed about 100 civilians in the first few weeks of the year.
"The FDLR have a very ugly past, but we haven't seen this level of violence in years," Anneke Van Woudenberg, a senior researcher in the Africa division at HRW, said.
Joseph Kabila, the Congolese president, also invited the Ugandan army to hunt Ugandan rebels of the Lord's Resistance Army (LRA) in the northeast of the country.
But last month he said both Ugandan and Rwandan soldiers had until the end of February to complete their operations, after domestic criticism and fears of abuse and looting.
Attacks on civilians by the LRA increased as a result of the Ugandan offensive, Reuters news agency said on Wednesday. Uganda is seeking an extension to its operation.