A gang of men widely believed to be Rwandan Hutu rebels raided the village of Mtulumamba on Saturday night. "Thirty nine civilians were burnt alive after being locked in their huts," said Sylvie van den Wildenberg, a spokeswoman for UN peacekeepers in Congo.
Fifty Pakistani peacekeepers were dispatched to the area immediately after the attack in the village 45 miles from Bukavu, the main town in Sud-Kivu.
A member of the UN team said: "Ashes remained where the 10 huts had stood, there were a couple of mass graves, where they had been buried. We were told the attackers locked the women and children in their huts while the men ran away."
Some locals said the raid was in retaliation for a Congolese army attack on rebels, while others said it was to discourage people from supporting the UN which has stepped up its activity in Sud-Kivu.
The main Rwandan rebel group in Sud-Kivu, the FDLR, is deeply split into factions and local militias who constantly shift alliances. The Hutu rebel leader, Ignace Murwanashyaka, in exile in Brussels, denied ordering the massacre, and claimed it was probably the work of a splinter faction.
An FDLR spokesman in Bukavu, Edmund Ngarambe, blamed the attack on another faction of Rwandan rebels, known as the Rastas. Many observers, however, say the two groups maintain close links.
Several rounds of negotiations and a UN-sponsored voluntary disarmament programme have achieved little in eastern Congo since a peace deal in 2002 ended the war that left nearly four million dead.
In May, the UN blamed Hutu rebels for the kidnap and rape of about 900 people since June last year.
Up to 15,000 rebels are believed to be active in the area where UN peacekeepers began patrolling only recently. The Hutu rebels fled across the border from Rwanda to seek refuge in the dense forests after the 1994 Rwandan genocide.
Their presence is a major challenge to the UN peacekeepers, who have long been accused of failing to protect civilians. UN soldiers and the Congolese army have threatened to disarm the rebels by force if necessary.
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