"MSF denounces this clearly unacceptable abuse of humanitarian aid for military purposes," said the organisation in a statement.
The medical charity was vaccinating thousands of children against measles on October 17 at seven sites in the rebel-held Masisi district in eastern DR Congo when the national army launched attacks, forcing the women and children to flee.
"Scattering everywhere, they are now in unknown locations and thus cannot be vaccinated," said MSF.
"We feel we were used as bait," said Luis Encinas, 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."
MSF said that in keeping with standard procedure, the aid group had informed parties including the Democratic Forces for the Liberation of Rwanda (FDLR) rebel group, the Congolese government and UN peacekeepers, of the immunisation programme before starting it.
"It is this neutrality that makes it possible for MSF teams to vaccinate in such FDLR-controlled zones, which, until that point, had been inaccessible to Ministry of Health staff," it said.
However, such attacks "seriously compromise our neutrality," said Encinas.
MSF also noted that there have been a "worrying increase in attacks against" aid groups in the eastern provinces of Nord-Kivu and Sud-Kivu.
"MSF demands that all parties to a conflict respect the work of humanitarian organisations. If not, it is the populations who pay the price," said Meinie Nicolai, MSF director of operations.
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