Responding to Friday's attack, the head of the World Health Organization (WHO), Tedros Adhanom Ghebreyesus, wrote on Twitter.
At least a dozen are fighting near Beni which is the epicenter of the second most serious EBOLA outbreak in history.
The WHO staffer killed was not immediately identified. He said the militiamen erroneously believed that foreigners had brought the disease with them to Congo.
Local organisations have said the number of Ebola deaths is rising.
"We are outraged by this attack - health workers and health facilities must never be targets", said WHO Director-General Tedros Ghebreyesus.
Congo's health ministry confirmed the assault on the Catholic University of Graben hospital.
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The latest attacks come a few days after Congo President Felix Tshisekedi visited the Ebola outbreak zone, pledging more military and police protection for health workers and asking residents for their cooperation. Doctor Valery Mouzoko Kiboung was an epidemiologist deployed by World Health Organization in response to the outbreak of the deadly Ebola virus disease that began last August, in the eastern North Kivu area of DRC, which is home to dozens of armed groups.
How to take community concerns into account while effectively containing Ebola remains the subject of debate, while worries are high that the outbreak could spread from the densely populated region to the major crossroads city of Goma or into nearby Uganda or Rwanda.
On March 9, an attack on a treatment centre at Butembo left a policeman dead and a health worker wounded.
Also weighing in on the attack, DRC health minister Oly Ilunga, MD, said on Twitter that national and worldwide health officers show courage and exceptional self-sacrifice to protect the DRC against Ebola, "sometimes at the cost of their lives". The president hoped to see the outbreak contained in less than three months, although some health experts estimate it could take much longer if community resistance continues.
He's committed the Congo to joining the worldwide coalition against the group.
In North Kivu and Ituri, around 1,300 people have already contracted Ebola, and more than 850 have succumbed to the virus.