Nkunda, who is ethnic Tutsi, reportedly entered the park in pursuit of Rwandan Hutu rebels, who may be hiding there.
The rebel leader maintains that the Congolese government is collaborating with the Hutu-led FDLR (the French initials for Democratic Liberation Forces of Rwanda). The FDLR is accused of involvement in the 1994 genocide against the Tutsis in Rwanda.
According to the United Nations, some 10,000 refugees have fled into Uganda following the latest fighting.
The UN has about 17,000 peacekeepers in the DRC, the largest such force in the world.
Amid the threat of poachers and armed militia groups, rangers in Virunga have struggled to protect the gorillas.
More than 120 guards have been killed in the last ten years.
On Thursday last week a ranger was shot and killed in an attack on patrol north of the town of Rutshuru, north of the city of Goma (DRC map).
Meanwhile, nine gorillas have been killed this year. Two gorillas are still missing.
The worst attack occurred on July 22, when five gorillas, including a silverback, were killed execution style. (Watch video report on gorilla executions.)
While conservationists link that massacre to the burgeoning illegal charcoal trade in the park, the killings of two lone males in January were widely attributed to General Nkunda's troops. (Read "Mountain Gorillas Eaten by Congolese Rebels". Warning: graphic picture.)
After the January killings, Nkunda met with park officials, pledging to make sure his men did not kill any more gorillas.
Emmanuel de Merode, the director of Wildlife Direct, says he does not believe the rebels are specifically targeting the gorillas. But he says the apes face enormous peril, as do the rangers.
"The gorillas happen to live in one of the worst areas of the world for conflict that is strategically important for armed groups," he said in a statement.
"We fear for the safety of these endangered creatures."
Conservationists received further bad news this weekend when the infant of Bilali, the only female from the Munyaga family of gorillas, was found dead.
The death of the baby gorilla is believed to be linked to fighting between two competing male gorillas.
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