The Congolese army operations in the area have been suspended
The Democratic Republic of Congo army has used vaccination clinics as "bait" to attack civilians, says aid agency Medecins Sans Frontieres (MSF).
Thousands of Hutu civilians were targeted when they visited sites set up to combat a measles epidemic, in areas controlled by the rebels, MSF said.
It denounced the attacks in North Kivu as "an abuse of humanitarian action".
On Monday the UN withdrew its support for a government army unit, accusing soldiers of killing 62 civilians.
MSF said the clinics were targeted despite security guarantees from all parties to enable the mass immunisation scheme to be carried out in the Maisisi district north-west of the city of Goma.
It said it was operating in support of the Ministry of Health, whose workers were unable to access regions controlled by the Hutu rebel group, the FDLR.
"We feel we were used as bait," said Luis Encinas, head of MSF programmes in Central Africa.
"How will MSF be perceived by the population now? Will our patients still feel safe enough to come for medical care?"
The targeting of civilians has been a major concern for charities operating in DR Congo and UN support for the government had been dependent on it respecting the neutrality of civilians.
The Congolese government says military operations in the area have been suspended to allow an inquiry into the UN allegations that soldiers had killed civilians.
The UN had been helping the army tackle the FDLR since January 2009.
The rebels have been at the heart of years of unrest in the region.
Their leaders fled to the area in 1994 after being accused of taking part in Rwanda's genocide and have since been fighting with the local Tutsi population and government troops.