The increase shows an upsurge in the prevalence of the deadly mosquito-borne parasitic disease, but it was still unclear what was behind the increase in the number, MSF said ahead of world malaria day on Wednesday.
"It's very difficult to give a scientific answer ...(but) you have to imagine where these people are living, in swampy areas, with pools of water and bad drainage," MSF official Corry Kik said.
Such environments are breeding grounds for the mosquitoes that carry the disease.
The eastern region of the vast central African nation remains unstable nearly 10 years after the signing of a peace deal ending a civil war that killed millions.
Malaria is the leading cause of death in the DRC, killing nearly 300,000 children under five every year.
The medical charity said it had treated 45,000 malaria cases in the DRC in 2009 and double that in 2010.
In the first three months of 2012, MSF registered another 85,000 cases, suggesting that the figures continue to rise, Kik, who is medical coordinator for MSF's operations in the Congo's eastern province of North Kivu, said.
World Health Organisation data shows that malaria killed about 655,000 worldwide in 2010, the majority in sub-Saharan Africa. New research, however, suggests it killed twice as many as previously thought.
(Reporting by Jonny Hogg; Writing by Bate Felix; Editing by Michael Roddy)
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