A wave of attacks by rebels and militia on health officials fighting the latest Ebola outbreak in Democratic Republic of Congo is leading to a surge in reported cases as the response to the lethal disease weakens.

There have been 157 deaths, of which 122 have been confirmed as Ebola cases, in the outbreak, which was declared almost three months ago. The total of probable and confirmed cases has now reached 244, with 63 recovering from infection.

The outbreak is centred on the North Kivu and Ituri provinces, both wracked by armed rebellion and ethnic killing since two civil wars in the late 1990s.

In the city of Butembo, militia killed two members of the medical unit of the Congo’s army on Saturday. The same day, 11 civilians and one soldier were killed in the city of Beni, where scores of people have contracted the virus.

The rebels also attacked Congolese army positions and abducted a dozen children aged between five and 10. Another five people died in an attack near Goma, the capital of North Kivu, on Tuesday.

The new violence comes amid warnings from international health officials that the outbreak could worsen significantly unless the response to the lethal virus is intensified.

A boy receives the Ebola vaccine in North Kivu. Photograph: Olivia Acland/Reuters

It is unclear who carried out the recent attacks. The Allied Democratic Forces (ADF), an Islamist group based in Uganda but active in eastern DRC, has clashed with Congolese troops in the city of Beni in recent weeks.

Mai-Mai militia, comprising a number of armed groups that originally formed to resist Rwandan invasions in the 1990s, are also present in the region.

“Some rebel groups use surprise attacks while others attack from different towns at the same time to overstretch the army’s response,” Capt Mak Hazukay, Congolese army spokesperson in North Kivu, said. He said the army is doing everything possible to prevent further attacks on the civilians.

“We suspect the attackers are part of a new rebel movement we are yet to identify,” said Jules Tshikudi, an army spokesperson in Ituri province.

The military’s inability to prevent attacks has led to anger and suspicion.

“How can you fight a group of rebels for weeks without knowing who they are?” Guy Mirimo, a resident of Djugu in Ituri, said. “This is not normal in a country with a working intelligence service.”

The number of cases of Ebola has accelerated in the past two weeks. Half have been in and around Beni, where the response was disrupted last month by a period of official mourning following attacks by armed groups.

“At the moment the outbreak is active in Beni and Butembo and the reaction team is focusing there. We are beginning to see results, especially in terms of the rise of alerts and cases,” Dr Bathé Ndjoloko, the coordinator of the response to the outbreak in Beni, told the Guardian.

More than 11,000 people who have come into contact with an infected individual have been traced, with around 5,000 still under surveillance. More than 20,000 people have been vaccinated so far.

Congolese and World Health Organization officials wear protective suits as they prepare equipment before vaccinating against the Ebola virus in the DRC. Photograph: STRINGER/Reuters

Several areas which had seen significant numbers of cases of the disease now pose little threat following intensive efforts by health officials and NGOs.

Attacks by rebel groups have repeatedly disrupted treatment, burials and vaccination programs in recent weeks but also reinforced suspicion of the authorities.

“The confidence of the general population in the government is in crisis and this has an impact on our work … Every time there is a clash, all the work we have done to engage the local community is wiped out, and without that we can’t beat Ebola,” Ndjokolo said.

On Tuesday, youths burned tyres in a protest following the killing of a civilian by suspected ADF fighters near the town of Oicha.

Following Saturday’s violence, protests erupted across Beni on Sunday morning with local people carrying the bodies of three of the victims through the streets.

Guillaume Saliboko, a law student, said some local people had set up roadblocks in Beni’s main street to make their anger known.

“We can’t understand how the ADF rebels can kill us in the middle of the town every time,” he added.

The town hall and a post office were targeted.

Analysts blame the upsurge of violence on intensified instability caused by competition between political actors in the east of the DRC in the run-up to forthcoming elections in December.

The mayor of Beni, Nyonyi Masumbuko Bwanakawa, said some community members were putting themselves at risk by refusing to be vaccinated.

“Fighting Ebola is a community responsibility but some residents go against advice from health officials which makes the rate of the spread of the disease go high,” he told the Guardian.

The health ministry said that in Butembo a group of 22 men dug up the body of an Ebola victim to make sure organs had been removed from the corpse by the health workers, in doing so entering into contact with bodily fluids of the victim. They all accepted to be vaccinated on Sunday, the ministry said.

Last month the WHO said the outbreak is expected to last several months and could spread to Uganda or Rwanda.

Both were well prepared for a rapid response, officials said, but neither had approved the vaccine currently being used in DRC.

The biggest recorded outbreak of Ebola killed an estimated 11,300 people across Guinea, Liberia and Sierra Leone, from 2014 to 2016. The disease was first seen near the northern Ebola river in DRC in the 1970s.

Additional reporting by Fiston Mahamba, Goma, and Ignatius Ssuuna, Kigali