The medical aid group has temporarily suspended its operations at two of its centres after attackers set fire to them.
The charity says the Ebola response must change - no more coercion to track and treat patients, and more choice for families on how to manage the disease.
Congo's Ebola epidemic has killed almost 600 people, making it the second deadliest in the world.
This is the second largest Ebola outbreak on record causing a massive global response.
Efforts to end the Ebola outbreak in the Democratic Republic of Congo, the second-largest such epidemic ever, are failing because outside organizations have alienated the communities, leading residents to avoid medical care and even to attack treatment centers, Dr. Joanne Liu, the worldwide president of Doctors Without Borders, said Thursday.
The use of police and the military to force communities to comply with Ebola care and prevention measures has been condemned by one of the organisations at the forefront of efforts to bring the current outbreak under control. "The communities are not the enemy".
"The police and the army are not involved in Ebola response activities and their role has never been to enforce sanitary measures".
A spokeswoman for the DRC's health ministry said there was a "misunderstanding" about the role of security forces in dealing with the outbreak, however, and rejected the MSF's claims as a "gross exaggeration of the situation".
The Interior Ministry has been asked to guarantee security, as it is unacceptable for health officials to be threatened and attacked, or for the threat of violence to stop families burying their loved ones in a dignified and safe manner, she said.
MSF, which is active across DRC, is considering whether to resume activities in the two areas, but is intent on avoiding the use of security personnel on site or in rounding up patients, Liu said.
"Contrary to global agents, local health workers don't have the privilege of being evacuated when security conditions worsen".
The epidemic is taking place in a region of the world wracked by armed conflict for decades.
Liu described aspects of the DRC's forceful Ebola response that would seem terrifying to villagers: fleets of vehicles arriving to pick up a sick individual, people instructed to wash their hands but not given soap, dead bodies sprayed with chlorine and unceremoniously buried in plastic bags while their possessions are burned to keep Ebola from spreading. A myriad of armed groups operate in eastern Congo, complicating efforts for the teams that go out into the communities to identify suspected cases of the disease. The outbreak, which started, last year, has killed more than 500 people in North Kivu and Ituri provinces.
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