General Laurent Nkunda, a Tutsi who heads the National Congress for the Defence of the People (CNDP), has defied calls from the UN Security Council to respect a UN-brokered January ceasefire.
Nkunda says his men are fighting to protect ethnic Tutsis.
UN officials also used helicopters in December to repel the group, killing hundreds under their mandate to protect civilians.
Earlier in the day, thousands of civilians attacked a UN compound in Goma angry at the failure by the peacekeepers to protect them.
But Michele Bonnardeaux, another UN spokesman, told Al Jazeera that "things have calmed down now", adding that the peacekeepers attacked the rebels to prevent them from entering Goma and further endangering the lives of cilivians.
"Our mandate is to support the national army in their effort to protect civilians there," he told Al Jazeera.
|Thousands have been displaced in Congo's fighting [Al Jazeera]
Meanwhile, the commander of the peacekeepers resigned on Monday after just seven weeks in the job, the UN said.
Lieutenant-General Vicente Diaz de Villegas "has indicated that for personal reasons he will not be able to continue with his assignment as planned," the UN told a regular news briefing.
The appointment of Diaz as the commander of Munoc, the French acronym for the force, was announced on September 9.
The UN said Diaz, a Spanish national, would be replaced as soon as possible, and that Brigadier-General Ishmeel Ben Quartey of Ghana would serve as acting commander.
In a separate statement, a UN spokeswoman said Ban Ki-moon, the UN secretary-general, was extremely concerned by the deteriorating situation in eastern Congo and called on the government and provincial authorities to restore calm.
Ban "reaffirms that Monuc will take all necessary measures within its mandate to protect civilians and United Nations personnel and property," she said.