The offensive against forces loyal to William Amuri Yakutumba, a deserter fighting President Joseph Kabila, saw thousands of Congolese crossing Lake Tanganyika into Burundi as clashes raged between government forces and Yakutumba rebels in the eastern province of South Kivu.
"The operation was a success, the rebels have been annihilated. There is no more fighting and we are in the midst of cleaning up operations," said army spokesperson Major Louis-Claude Tshiwanga.
He said since the launch of the operation on January 21, "48 Yakutumba have been killed and 150 captured".
The army paraded the captured rebels as well as cannons and machineguns seized during a press conference on Thursday in the town of Uvira.
The Yakutumba attacked Uvira at the end of September in a naval operation before being pushed back from the area by MONUSCO, the UN mission in the Democratic Republic of Congo.
The army spokesperson said people were slowly returning to the town.
Security sources said the rebel chief had not been captured but could have been wounded in fighting last week.
KEEP UPDATED on the latest news from around the continent by subscribing to our FREE newsletter, Hello Africa.
FOLLOW News24 Africa onTwitterandFacebook.
But the UN radio Okapi, citing General Philomen Yav who was in charge of the offensive, said 83 rebels and six government soldiers had died in the fighting.
"Almost all the territory under the control of the Yakutumba has been recovered," the radio said.
The DRC government has announced it is waging "war" against two militias in the east - the Yakutumba and the Ugandan Islamist rebels of the Allied Democratic Force (ADF).
The Congolese Yakutumba are in South Kivu while the ADF are active in North Kivu.
Both regions border Uganda, Rwanda, Burundi and Tanzania.
Rival militia groups have long held sway over large areas in the two provinces, often competing for their rich mineral resources.