Relatives of a patient were part of the crowd that stormed the Nyakunde Hospital in Ituri province on Wednesday afternoon and evening, throwing stones and damaging its perimeter fence, said François Berocan Uderos, a medical biologist at the hospital.
The crowd was responding to the death of a woman who had gone to the hospital to give birth but developed severe anaemia, he said.
"Members of her family offered to donate blood but the hospital refused because blood transfusions are prohibited during an Ebola outbreak," Uderos said.
The woman died about 3pm and the attack on the hospital began shortly afterwards, he said, adding that several of the up to 10 Ebola patients receiving treatment there had left.
"The medical team has since left the hospital. The generator supplying power to the facility is no longer functioning, and patients have fled," he said.
The attack underscores the difficulties health authorities face in tackling Ebola in eastern DR Congo, where mistrust of medical teams, community resistance and insecurity have repeatedly disrupted treatment and containment efforts.
The latest Ebola outbreak, DR Congo's 17th, has so far led to 2073 confirmed cases and 796 deaths, according to official figures.
There have been several attacks by angry crowds on health facilities since the outbreak was announced in May, recalling violence that unfolded during a 2018-2020 outbreak in eastern DR Congo that killed more than 25 health workers.
The security risks have fuelled protests and strike threats by health workers who say the pay they receive does not reflect the workload and stress they endure.
Samaritan's Purse, a Christian aid group that has an Ebola treatment centre next to the facility in Nyakunde, removed its staff as the situation deteriorated on Wednesday, the group's vice president Ken Isaacs said.
"We evacuated our people and those well enough in the ETC (Ebola treatment centre) got out and ran. All of Samaritan's Purse got out and we haven't gone back since. There are roadblocks and we don't feel it is safe," Isaacs said.
Some patients who were too sick to flee remained behind and were "left without treatment," said Isaacs, who was briefed on the incident by staff.
There were three Ebola patients at the facility on Thursday morning, Uderos said.
DR Congo's army said in a statement that it had opened an investigation of unrest in Nyakunde.
The outbreak is disrupting negotiations linked to a major US-backed minerals partnership in the country, four people familiar with the matter told Reuters.
The US State Department said it was working to contain the outbreak while advancing the minerals partnership.
