The incident occurred in the Ebola-plagued region during clashes between UN peacekeepers from the MONUSCO mission and the Allied Democratic Forces (ADF) militia on Friday night.
“It was in exchanges of fire that the house was hit by a shell”, Michel Yao, WHO’s co-ordinator for Ebola response operations in Beni, told AFP.
No one was injured, he said, adding that it was not known whether the shell came from the militia, the UN peacekeepers or the Congolese army backing them.
The 16 WHO workers, out of a total of 191 in Beni, were “traumatised” and left for the eastern city of Goma on Saturday to “de-stress”, Yao said.
“It’s a two-storey house and the staff took refuge downstairs. The shell landed on the roof of a toilet,” he said.
It was the first time WHO has had to evacuate staff from Beni, where an Ebola outbreak has killed 213 people since August 1.
Earlier Saturday, DR Congo’s health ministry announced that efforts to fight the deadly virus in Beni had been suspended after clashes just a “few metres” from a local emergency centre and hotels of several response teams.
The ministry said that the UN and army forces had repelled the attack by the ADF, a shadowy armed group that has killed hundreds of people since 2014 and at least seven peacekeepers in clashes just this week.