The deal calls for the rebels to withdraw towards the town of Kibumba The M23 rebels deserted from the army in April, with some 500,000 people fleeing their homes in ensuing unrest.
Who are the M23 rebels?
Named after the 23 March 2009 peace accord which they accuse the government of violating
This deal saw them join the army before they took up arms once more in April 2012
Also known as the Congolese Revolutionary Army
Mostly from minority Tutsi ethnic group
Deny being backed by Rwanda and Uganda
Believed to have 1,200 to 6,000 fighters
International Criminal Court indicted top commander Bosco "Terminator" Ntaganda in 2006 for allegedly recruiting child soldiers.
The UN and US imposed a travel ban and asset freeze earlier this month on the group's leader, Sultani Makenga.
The UK has suspended aid to Rwanda, amid concerns about the country's role in the conflict.
Both Rwanda and neighbouring Uganda strongly deny UN accusations that they are backing the M23.
Reports on Saturday spoke of a number of flat-bed trucks carrying several hundred rebels out of Goma.
Some 1,500 M23 fighters were reported to have occupied the city.
M23 deputy spokesman Amani Kabasha told Reuters: "The M23 is leaving Goma."
According to the withdrawal accord, mediated by Uganda, the rebels are to pull back to a 20km (13 mile) buffer zone around Goma.
The accord had stipulated that the M23 would leave behind 100 soldiers to guard the airport in conjunction with a UN contingent and a government unit.
However, Sy Koumbo, a spokesman for the UN in Congo, told Associated Press that the rebels had tried but failed to force their way into the airport to seize weapons on Friday.
The rebels said recovering the materiel was part of the withdrawal process.
More than 270 Congolese policemen have arrived in Goma's port as part of the transition.
The UN has warned of a growing humanitarian crisis in the region because of the recent fighting.
Goma is the key city in an eastern border area that has seen years of conflict sparked by ethnic and political differences, and grievances over mineral resources.
Some five million people died during the 1997-2003 DR Congo conflict, which drew in several regional countries, including both Rwanda and Uganda.