Ebola responders are on lockdown in the Democratic Republic of the Congo after angry residents stormed a UN peacekeepers camp in protest at fatal militia attacks on civilians, the World Health Organization has said.

On Tuesday, the WHO evacuated 49 non-essential staff out of the 120 people working on the epidemic in the city of Beni in North Kivu, one of the recurring Ebola hotspots.

The UN children’s fund, Unicef, also temporarily evacuated 27 staff, leaving 12 in Beni, Reuters reported. Some NGOs suspended their operations temporarily.

Each day that insecurity prevents responders accessing people in affected areas is a “tragedy” that prolongs the second worst outbreak of the disease ever recorded, said the WHO’s director general, Tedros Adhanom Ghebreyesus, in a tweet.

Tedros Adhanom Ghebreyesus (@DrTedros) Each day that we don’t have full access to all #Ebola-affected areas in #DRC we cede ground to the virus, prolonging the outbreak.

This is a tragedy because it will only add to the suffering of already overburdened communities.

The Ebola outbreak, which has killed 2,198 people, is centred in the volatile north-east of the country. The number of confirmed cases has decreased over recent months and last week the WHO recorded an all-time low of just seven cases. But staff said that whenever there is conflict, the numbers go up again.

On Wednesday, AFP reported that six people have been killed in protests so far this week. The bodies of four young protesters were found near the UN base in Beni after an attack on Monday in response to the killing of eight civilians. Six Congolese soldiers were wounded by gunfire, the Associated Press said.

“Our demonstration is patriotic,” one of the demonstrators in Wednesday’s protest, law student Fiston Muhindo, told AFP. “Monusco is standing on the sidelines as the massacres unfold, when its chief mission is to protect civilians.”

Dozens of protesters, many of them young, invaded one of two UN peacekeeper camps in Beni on Monday, tearing down a wall despite shots fired by the Congolese security forces in an effort to disperse the crowd. Some demonstrators demanded that the UN mission act or leave, and UN staff were evacuated to another base, near the airport. In Goma, police used teargas to break up a demonstration outside the university.

After an emergency meeting with the UN, the Congolese president Félix Tshisekedi decided to allow joint operations between national and UN forces against the Allied Democratic Forces, a militia group operating near the Ugandan border that has plagued eastern DRC for decades.

Facebook Twitter Pinterest A man reacts after the burned corpse of a friend was found beneath a house in Beni following an alleged attack by ADF rebels. Photograph: John Wessels/AFP/Getty Images

Since 5 November, 81 civilians have been killed in the region, according to Agence France-Presse. The Congolese army began an offensive against the ADF on 30 October, vowing to wipe out armed groups in the east of the country.

Following Monday’s attacks, a UN spokesman said peacekeepers could not intervene, because the Congolese army had launched its offensive unilaterally.

Seif Magango, Amnesty International’s deputy director for east Africa, the Horn and the Great Lakes, said the security and UN forces were “utterly failing” in their duty to protect the citizens of Beni and other hotspots in DRC.

Magango said: “It is scandalous that civilians are dying day in, day out while the local police and nearby UN peacekeepers stay put in their camps. It is high time all entities charged with civilian protection in the DRC, including the UN mission, take steps to fulfil their mandate and bring an end to these killings.”

Matthias Gillman, a spokesman for Monusco, one of the biggest peacekeeping operations in the world, said staff had been redeployed to another camp on the outskirts of Beni. Gillman said the mission had not been involved in operations against the ADF so far but that this would change.

Asked to respond to accusations that the UN was failing civilians, Gillman said the “modus operandi” of the militia, to carry out random attacks at night in remote jungle villages, made its mandate to protect civilians difficult. The UN also had a duty to fight armed groups, he said, but had been prevented from doing so because the Congolese army had begun operations against the group unilaterally.

“We understand the attacks going on by ADF are unacceptable and we are not indifferent,” Gillman said. “Our mandate is to protect civilians but to fully implement that is very complicated.

“Our head of mission at Monusco met with the president to see how we can better coordinate our activity and do a better job of getting rid of ADF.”

Facebook Twitter Pinterest People in the North Kivu city of Oicha wield sticks and machetes as they search for ADF rebels. Photograph: John Wessels/AFP/Getty Images

Margaret Harris, a spokesperson for the WHO, was evacuated from Beni on Tuesday after her vehicle came under attack, with rocks and bricks shattering the window.

Speaking from Goma airport, she said: “Amazingly, a lot of work is still going on in the hotspots. But the problem is a lot of people – around 300 – who are at high risk related to one particular infected individual, have not been contacted. Especially yesterday when there was gunfire and riots. It could build up again.”

World Vision, which has 35 staff, 30 of whom are local, running community programmes against Ebola, said its staff were also on lockdown.

Helen Barclay-Hollands, World Vision DRC eastern zone director, said operations in Beni had been completely halted and that efforts to control Ebola and measles, which has killed 5,000 people, were at serious risk of being undermined. Children would die from disease if work did not resume extremely quickly, she warned.

Facebook Twitter Pinterest Chamim, whose mother recently died of Ebola, cries at a Unicef centre in Beni for children whose families have fallen prey to the disease. Photograph: Zohra Bensemra/Reuters

“This outbreak of violence could not have come at a worse time,” Barclay-Hollands said. “Now this is all at risk.”

Other NGOs said the Ebola outbreak should not be allowed to overshadow the “long-lasting humanitarian crisis” in DRC, driven by conflict, which is severely underfunded. A total of 12.8 million people in DRC need urgent support.

Whitney Elmer, Mercy Corps’ country director in DRC, said: “For the past year, the Ebola outbreak in eastern DRC has overshadowed the complex and long-lasting humanitarian crisis in the country. We have seen donors pivot resources and lose focus of the wider humanitarian needs, but with 15 million people projected to be in need of emergency relief in DRC in 2020, this cannot continue.”