The global organisation's president, Joanne Liu, told reporters in Geneva on Thursday that there have been some "30 different incidents and attacks against elements of the response".
Last week Medecins Sans Frontières (Doctors Without Borders) suspended medical activities at the focal point of the epidemic after two facilities were torched by unidentified assailants.
Liu criticized the militarization of the situation, saying Thursday that police and security forces are trying to force people to comply with health authorities. More than 40% of Ebola deaths are still taking place in communities rather than at treatment centres, according to the group.
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.
Liu said the problem is exacerbated by heavy-handed DRC government tactics that amount to dragging reluctant villagers into medical centers for involuntary treatment.
There were signs the outbreak - the second worst ever - was not being brought under control.
The epidemic is the second-largest ever, after the one in Guinea, Liberia and Sierra Leone from 2014 to 2016, which sickened 28,610 people and killed 11,308.
It also means that untold numbers of people around these patients have been exposed and may have contracted the disease.
The MSF International president says that people are dying so consistently of Ebola, citizens in the community of Congo are losing trust in doctors to help. "The police and the army are not involved in Ebola response activities and their role has never been to enforce sanitary measures".
An attack by gunmen on one of the centres last week in Butembo forced its temporary closure, but the health ministry said on Monday that the centre would reopen.
"Ebola responders are increasingly seen as the enemy", Liu said.
In addition, Liu said, 35 percent of the new cases are in people who had not previously been identified as contacts.
She added there was a need for caution, however, with the "high mobility of the population" and the "spread of misinformation and rumours" about the medical response creating a risk of further infections. It has an incubation period of between two to 21 days, according to the WHO.
"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.