This follows attacks on two of its treatment centers last week.
"Using police to force people into complying with health measures Is not only unethical it's totally counterproductive", she said.
The report said the tensions have caused people to avoid bringing people infected with Ebola to treatment centers and more than 40 percent of the deaths are still taking place in communities rather than at the centers.
The centre in Butembo, the epicentre of DR Congo's latest Ebola outbreak, is now run by the health ministry in collaboration with the World Health Organization (WHO) and the United Nations children's organisation Unicef, the authorities said.
Despite telling the DRC military that their treatment centres are a military-free zone armed personnel continue to bring patients in, MSF said. "It shows how the response has failed to listen and act on the needs of those most affected", warned MSF President Joanne Liu.
The MSF global president stressed that people were facing the biggest Ebola outbreak in the history of the country as "907 people have fallen sick from Ebola, 569 of them have died".
The worst-ever outbreak, which was centred in West Africa from 2013 to 2016, killed more than more than 11,000 people. Vaccination for Ebola must reach more people, and more vaccines are needed for this.
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".
"Ebola still has the upper hand", Liu said.
Three Canadians - one doctor and two nurses - were working in those centres but are safe.
Involvement of security and police forces merely deepened suspicions that Ebola was being used as a political tool, she said.
"Contrary to global agents, local health workers don't have the privilege of being evacuated when security conditions worsen".
"We have a striking contradiction", said Liu.
It has claimed 561 lives out of 894 recorded cases, according the latest DRC health ministry figures.
"We have seen outbreaks end in areas where the communities have become engaged, from health workers to religious leaders to youth groups", Jasarevic said.
"We can share the right messages but if you have counter messages that makes it hard", Ilunga said.
"In every town, partners work with social scientists, anthropologists and local leaders to understand the context and tailor the approach to what works", he added.