Staff of the World Health Organization (WHO) were forced to leave as a shell hit the building they were in.
It is not clear when the mission might resume.
The health ministry blamed the emergency centre attack on the Allied Democratic Forces (ADF), a Ugandan Islamist militant group that has been active since the 1990s.
But it was not clear who had fired the shell that hit the house where 16 WHO staff were staying. It hit during exchanges of fire, and could have come from the militia, the UN peacekeepers or the Congolese army.
The staff members took refuge downstairs, before evacuating Beni for another city.
Health officials in the region stopped giving vaccinations and other outreach work two months ago after a rebel attack in which 18 people died.
Seven UN peacekeepers and 12 Congolese soldiers were killed earlier this week during a joint operation against the ADF.
An Ebola outbreak in the region has killed more than 200 people since August.