Cameroonian doctor Richard Mouzoko was shot dead in April at a hospital in Butembo, where he was treating Ebola patients.
The “passionate” medic was “always ready to go where people would need his help most,” the WHO said in a tribute.
The motive for the attack is unclear.
More than 1,800 people have died from the Ebola virus in the past year. Efforts to contain the spread have been hindered by militia group violence and by suspicion towards foreign medical assistance.
Senior military prosecutor Lt Col Jean-Baptiste Kumbu told AFP that militiamen involved in attacking treatment centres, including Butembo hospital, had under interrogation implicated four doctors in planning the raids.
He said the three Congolese doctors will be prosecuted for “terrorism” and “criminal conspiracy”, according to AFP, while the fourth doctor was still at large.
The current outbreak in eastern DR Congo began in August last year and is the biggest of the 10 to hit the country since 1976, when the virus was first discovered.
It is dwarfed by the West African epidemic of 2014-16, which affected 28,616 people mainly in Guinea, Liberia and Sierra Leone. About 11,310 people died in what was the largest outbreak of the virus ever recorded.
Dr Mouzoko was one of a number of medics deployed by the WHO to help fight the spread of the virus in DR Congo.
Former colleagues in Madagascar, Cameroon and DR Congo have described Dr Mouzoko as a committed professional, who over the course of his career, helped train hundreds of young doctors and health workers.
“He would regularly spend 15 to 20 days a month working among isolated communities in his home country, Cameroon, far from his wife and 4 children,” the WHO said in a statement after Dr Mouzoko’s death.
His funeral in April was attended by the global health body’s top official and its Africa director.
In a letter to the mayor of Butembo, a group representing local doctors said it was “indignant” over the arrests, adding that their absence would cripple vital medical services in the area such as blood transfusions and disease prevention.
The group has threatened to strike within 48 hours unless the three detained doctors are released.
But the military prosecutor dismissed their demands as “out of the question”, AFP reports.
Why are Ebola workers being attacked?
About 200 health facilities have been attacked in DR Congo this year, forcing health workers to suspend or delay vaccinations and treatments.
Reuters quotes Lt Col Kumbu as saying a total of 54 people are currently under arrest in connection with attacks on Ebola treatment centres.
In February, medical charity Médecins Sans Frontières (MSF) put its activities on hold in Butembo and Katwa – two eastern cities in the outbreak’s epicentre.
In North Kivu, community-based militia groups called Mai-Mai have been behind some of the attacks against health centres and workers.
Another militia group, the Allied Defence Forces (Ugandan rebels operating within DR Congo) have also been accused of causing widespread disruption to medical units.
There have also been a series of attacks by other unidentified groups on Ebola response centres.
In one incident, family members assaulted health workers who were overseeing the burial of their relative in May.
A 2018 study published in the Lancet medical journal says “belief in misinformation was widespread” concerning the Ebola outbreak in North Kivu.
One in four respondents believed in the statement that Ebola does not exist, with an even higher proportion saying the Ebola outbreak was fabricated for financial gain, or to destabilise the region.
“There’s already been civil unrest in the region and that’s exacerbated when a foreign response comes into an area that’s heavily guarded,” says Lara Salahi, an author who has written about responses to Ebola outbreaks.