"We are now extremely concerned that several factors may be coming together over the next weeks and months to create a potential ideal storm", the WHO's head of emergency response, Peter Salama, told a news conference in Geneva. "A flawless storm of active conflict, limiting our ability to access civilians, distress by segments of the community, already traumatized by decades of conflict and of murder".
Saturday's attack was pinned on the Allied Democratic Forces, an Islamist group, in local media reports, though with dozens of armed militias active in eastern Congo, establishing culpability is hard.
Ebola has claimed 100 lives since the deadly virus outbreak started almost two months ago in North Kivu, a north-eastern border region where more than 100 armed groups operate.
"The front line is no longer in the Virunga National Park and is now in Beni, which poses a real danger for the holding of safe elections on December 23", said Anselme Mwaka, an opposition MP from the Union for the Congolese Nation (UNC).
The city has declared a "ville morte", a period of mourning until at least Friday, obliging World Health Organization to suspend its operations.
"We can see the hallmarks of both local and external involvement in the "Somalisation" of Beni, despite efforts to reduce these killings", he said. "Our operations are in effect suspended", he added.
The development meant that on Monday, WHO staff were able to reach only 20 per cent of the contacts they wanted to, in and around Beni, Dr Salama said.
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"This points to an increasingly worrisome security situation across the country", the group said in a statement Monday. Some potentially infected people have fled treatment.
Although most people remained open to health workers, there has been a spread of "conspiracy theories" suggesting Ebola is part of a government plot or a sinister money-making scheme, which have curbed WHO's access to civilians, Salama said.
About 100 people have died and 150 cases of the virus have been confirmed across two vast provinces, North Kivu and Ituri. Ebola's symptoms include high fever and vomiting, which make it hard to treat, because it resembles many other illnesses in its early stages.
Local public health officials warned the unrest will have a "considerable impact" on the Ebola outbreak.
The Beni region, not far from the Ugandan border, is under siege from the Allied Democratic Forces (ADF), an Islamist rebel group blamed for hundreds of civilian deaths over the past four years.
"This has the potential to spiral", Salama said.