The latest Ebola outbreak, which causes haemorrhagic fever, vomiting and diarrhoea, is believed to have killed 99 people since July and infected another 48.
WHO's Emergency Response Chief and Australian epidemiologist, Peter Salama, told a news conference in Geneva that Ebola had claimed 100 lives since the deadly virus outbreak almost two months ago in North Kivu.
Public health teams are also investigating nine suspected cases not included among the 150, the ministry reported. The worldwide response was swift, however, and the outbreak was declared over in June with 33 deaths.
This is the second outbreak of Ebola in Congo this year.
"If WHO and its partners had to leave North Kivu ... we would have grave concerns that this outbreak would not be able to be well controlled in the coming weeks or months".
This progress risks being undone by the uptick in violence in the Kivus region, which is home to more than 100 armed groups, he said, before noting that neighbouring countries now also face an increased risk of the disease spreading.
"We will not yet consider the need to evacuate but we are developing a range of contingency plans to see where our staff are best located", he said. As a result, other health epidemics, including cholera, measles and polio, as well as human trafficking, are flourishing there.
The ADF rebels have killed more than 1,500 people in the Beni region since October 2014. A violent clash in Beni on Sunday led to the death of 18 people, General Bernard Commins, deputy commander of the UN peacekeeping forces, told Radio Okapi, a United Nations newscast.
Being on lockdown there, even for a few days, prevents health workers from the crucial work of tracing people who may have come into contact with Ebola, Salama warned.
Some residents of Beni have taken to the streets to protest against the security problems.
"All the pillars of the response remain fully operational", he wrote.
Though agencies continued the health work to contain Ebola, such attacks hamper those efforts. It came just months after the previous outbreak in May, which claimed the lives of 33 people.
The experimental rVSV-ZEBOV vaccine, made by pharmaceutical company Merck, proved highly protective against the deadly virus in a major trial in Guinea, according to WHO.