Forced to flee
Women and children were said to have been forced to flee. "They are now in unknown locations and thus cannot be vaccinated," MSF said.
"We feel we were used as bait," said Luis Encinas, the head of MSF programmes in Central Africa.
"The attacks coincided with the beginning of our vaccination and put the lives of civilians in extreme risk."
An army spokesman has questioned whether the agency had contacted the operation's headquarters before the attacks.
MSF said that it had told the government, Democratic Forces for the Liberation of Rwanda (FDLR) opposition group and UN peacekeepers about the clinics and received guarantees from warring factions that the vaccination programme could go forward.
A military spokesman for the UN mission in the Congo said it was not aware of the incidents.
Maynee Nicolai, MSF's Operational Director, told Al Jazeera: "We were working in the eastern side of the DRC ... our teams were aware in October of a measles epidemic [and] decided to vaccinate.
"We informed all different armed actors that we were going to vaccinate. We asked their security guarantees. And we explained exactly when and where we were vaccinating.
"Part was done on fixed sites in government held areas and part was done using mobile sites in rebel controlled areas.
"The day we came to vaccinate in rebel-controlled areas ... we were to vaccinate on seven sites. On the day we arrived the Congolese army opened fire on villages where the MSF teams were vaccinating.
"Our teams had to flee on foot into the hills," she said.
Nicolai added: "We are in continuous contact with the various groups."