Seven members of a Mai-Mai militia and a police captain were killed, Butembo Mayor Sylvain Kanyamanda said.
"Before this attack on Wednesday, leaflets of May-Mai militia were circulating to tell the teams of foreign doctors to leave the region as soon as possible before the worst happens," he told The Associated Press.
Ebola response work was again halted following the violence. Attacks on Ebola health centers already have forced Doctors Without Borders and other international aid organizations to leave. Last month an attack on a hospital in Butembo killed a Cameroonian epidemiologist working for the World Health Organization.
More than 1,000 people have died of Ebola in eastern Congo since the outbreak was declared in August. The volatile security situation has impeded efforts to control the virus' spread as health teams cannot safely go to all the areas where disease transmission is happening.
In addition, about half of the victims are dying at home instead of in a health facility where they would be isolated to prevent Ebola from spreading. These hidden cases have made it difficult for health teams to track the contacts of Ebola patients and vaccinate those most at risk.
Dozens of rebel groups operate in the region including Mai-Mai militias, and political rivalries in part drive community resistance to health workers.
Michael Ryan, WHO's emergencies chief, told reporters last week that there had been 119 attacks recorded since January including 42 directed at health facilities.
"Every time we have managed to regain control over the virus and contain its spread, we have suffered major, major security events," Ryan said. "We are anticipating a scenario of continued intense transmission" of the disease.
Associated Press writers Krista Larson in Dakar, Senegal and Saleh Mwanamilongo in Kinshasa, Congo contributed.