The refugees, 557 in all, boarded a United Nations Development Programme-chartered ship in Brazzaville for Kinshasa, capital of the DRC, across the River Congo.
An official delegation accompanied the former soldiers from the Zairean Armed Forces (FAZ) and their families on the trip. A second group were due to make the journey later in the week, a delegation member said.
Since mid-October, several hundred ex-soldiers who have been refugees in Congo since Mobutu's removal have been camped out at Brazzaville's river port in the hope of being repatriated.
The Kinshasa authorities had refused to take them back until they were all identified.