"All these areas which are without the army, without protection, have been seized again by the (Hutu rebel group) FDLR," said Jean Luc Mutokambali, a parliamentarian from the region and member of the ruling coalition.
"That's leading to self-defense groups like Raia Mutomboki," he said, referring to a local militia involved in the clashes whose name means "Angry Population".
The International Committee of the Red Cross said on Friday that it was treating scores of victims from the fighting.
"Most of the victims are civilians, some of whom are very young children, elderly people or women," Laetitia Courtois, a spokeswoman for the ICRC said in a press release.
"Some injured people had to be carried for hours on foot ... to reach healthcare centers."
Both sides in the fighting are targeting civilians, often suspected wives, families and friends of their enemies, said Marie Claire Bangwene Mwavita, the administrator of Masisi territory. She said several villages were recently pillaged near the border between North and South Kivu provinces, and at least four people burnt alive in their homes.
The United Nations local peacekeeping mission, known as MONUSCO, has deployed attack helicopters in North Kivu in an attempt to dissuade armed groups from targeting civilians, spokesman Lieutenant Colonel Mactar Diop said.
Ntaganda, a former rebel wanted by the ICC for war crimes and who was integrated into the army in a 2009 peace deal, mutinied with around 600 soldiers last month after the government said it would arrest him.
The fighting linked to his mutiny has forced some 100,000 people to flee their homes according to the UN, including thousands into neighboring Rwanda and Uganda.
A spokesman for Ntaganda's rebels said they are in control of the Runyoni area of North Kivu, near the border with Rwanda. Colonel Vianney Kazarama said the rebels had killed scores of Congolese soldiers in recent clashes and seized large quantities of arms, although the government has denied this.
Human Rights Watch said last week Ntaganda's group was recruiting children as soldiers.