It was the latest in a series of attacks on health workers and responders that authorities say is hampering efforts to slow the fastest-growing Ebola outbreak in the world.
The attack took place on Saturday in the town of Bafwasende in the country's eastern Tshopo province, WHO Director General Tedros Adhanom Ghebreyesus said in a post on X.
"Everyone working to protect communities from this deadly disease must be able to work in dignity and safety. Healthcare must always be protected," he said.
WHO regional director for Africa, Dr Mohamed Yakub Janabi, also condemned the attack on X.
"Misinformation and fear must never fuel violence," he said.
The country's health ministry's most recent data indicates more than 9,800 cases including more than 4,700 deaths have been recorded since the start of the outbreak in May, making it the deadliest Ebola outbreak in Congo's history.
In October a Congolese politician was beaten to death in North Kivu after publicly defending the government's response to Ebola. He had been calling on the public to obey response measures, particularly social distancing and handwashing.
It came after authorities launched a village-centred approach to fight the outbreak which faced resistance from some residents who dismiss Ebola as a hoax.
There is widespread distrust of the country's government because of how it has managed past Ebola outbreaks as well as chronic corruption.
Responders say scepticism about the disease among communities has complicated efforts to work with residents, including in remote areas and emerging hot spots that already face shortages of medical supplies and healthcare workers.
Back in May at the start of the outbreak, two tents at health centres were set alight in two separate attacks in just one week by angry residents.
Meanwhile, Ugandan citizens returning to the country with a history of travel to Congo would be quarantined for 21 days, Health Minister Chris Baryomunsi said on Sunday as Uganda tightened Ebola precautions.
Uganda says it is Ebola-free after declaring an end to its latest outbreak in July, but there has been concern among health experts after two people who had recently passed through the country later tested positive in Kenya and Nigeria.
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