According to Burundi army spokesman Major Adolphe Manirakiza on Saturday, at least 153 bodies had been counted. "What has happened is abominable," he said.
Burundi's Hutu rebel National Liberation Forces (FNL) claimed responsibility for the attack on the Gatumba camp on Friday.
Gatumba is located 20km west of the capital Bujumbura and just 4km from the DRC border.
An FNL spokesman said the raid on the camp followed several days of attacks against them by the Burundi military.
"We counter-attacked last night on the military camp and police brigade at Gatumba, and the soldiers withdrew into the refugee camp and the Banyamulenge fought along with them," rebel spokesman Pasteur Habimana said.
Most of the refugees at the Gatumba camp are Banyamulenge, people of ethnic Tutsi origin, who fled the Sud-Kivu region in eastern DRC earlier this year during an uprising in the town of Bukavu.
However, the FNL spokesman said the victims were fighters in uniform who had taken refuge inside the camp.
"Banyamulenge were killed, they were people in military uniform who were armed and who fired at us," he said. The attack began at 2000 GMT on Friday, a local official said.
Burundi is slowly emerging from a civil war that began in 1993 and has so far claimed about 300,000 lives.
Since a peace deal was struck last November, only the FNL has remained active against the power-sharing Hutu-Tutsi government, and 16 of the tiny country's 17 provinces are at peace.
The army and the Forces for the Defence of Democracy, the main former Hutu rebel movement, continue to mount joint operations against the FNL in rural Bujumbura, the province surrounding the capital.
President Domitien Ndayizeye
heads the Hutu-Tutsi government
Daily clashes continue in the province, according to the UN peacekeeping operation in Burundi, which on Friday called for an end to violence against the civilian population.
UN troops arriving
The UN mission said it had recorded "summary executions, acts of torture, sexual violence, and arbitrary detention by armed men, targeting innocent civilians" since their arrival in the country.
Carolyn McAskie, special representative for UN Secretary General Kofi Annan, urged all sides to observe an immediate truce, calling "on all warring parties to end the violence, respect human and humanitarian rights".
The UN mission arrived in Burundi on 1 June to take over from an African Union mission of 2400 troops. It will eventually have 5650 soldiers.