The panel was originally scheduled to begin its work on September 14, a week after the truce was signed.
Talks were initially postponed for a month because of demands made by the rebels, before the process started without them. The FNL wanted the government to release some of their members, including one of their nominees to the panel.
They also wanted the authorities formally to grant temporary immunity to their fighters and to clear the way for them to obtain Burundian passports.
Earlier this month, Bujumbura freed six FNL members and handed them over to Charles Nqakula, the South African mediator.
On Sunday, the rebels sent a 17-strong team to the panel. The government side is led Evariste Ndayishimiye, Burundi's minister of interior.
"We are not in the final step, but what encourages me is that guns have been silenced on the ground," he said.
"We are not in the final step, but what encourages me is that guns have been silenced on the ground"
Evariste Ndayishimiye, Burundi Minister of Interior
The committee started work after an opening ceremony in Bujumbura attended by Nqakula for South Africa, Mahmoud Youssef, the head of the UN Office in Burundi, and Mamadou Bah, the African Union envoy, among others.
The committee will work on establishing a new timetable for the integration of the ex-fighters into the army or the police and for the de-mobilisation of those who will be left out.
Burundi elected a power-sharing government in 2005 headed by Pierre Nkurunziza, the president and former Hutu dissident leader, after 12 years of civil strife which has thus far claimed some 300,000 lives.
The war erupted in 1993 with the assassination of Melchior Ndadaye, a member of the Hutu majority and the country's first democratically elected president, by elements of the then minority Tutsi-dominated military.