Rwanda invaded Congo along with Uganda in 1998, accusing the government of sheltering the perpetrators of Rwandaâ€™s genocide.
Angola, Zimbabwe and Namibia backed the Kinshasa government.
Analysts differ on their estimates of the number of Rwandan troops in Congo, with some putting the figure between 20,000 - 40,000 or even higher. Rwanda, seen as the most organised and powerful military force in the conflict, controls about a third of the former Zaire.
Some 500 soldiers were due to arrive in the capital Kigali in army helicopters after leaving the eastern Congolese town of Kindu, 500 kms (310 miles) to the west.
The overall withdrawal of Rwandan troops will take place progressively but rapidly, according to available funds and logistics, government officials said.
Rwanda Set For DRC Troop Pullout