WHO halted operations in parts of the Uige district in northwestern Angola on Friday following the attacks on Thursday.
Residents apparently feared the medics could be spreading the infection that has already claimed 184 lives, some of them health workers.
WHO officials said later on Sunday it had restarted the campaign in Uige, epicentre of the outbreak.
Angola's health department, releasing the latest toll figures, said there had been a total of 213 cases, making it the worst outbreak of the disease yet.
''Of course it has restarted," Fatomata Diallo, WHO's country representative, said when asked if WHO had since resumed its operations.
In this kind of outbreak control, security is crucial. If we find those kind of problems in all parts of Uige, we will stop (our operation). But it was only in one part of Uige that we found this problem," she said.
Diallo said WHO had been in touch with local officials and had received more support to help continue with its work.
WHO vehicles carrying 18 staff were attacked and damaged in Uige on Thursday, the WHO said on its website.
''We are very concerned because you can begin counting everyday lost in terms of how many people die. It's important to get this job done. Every day it is delayed is a problem," Richard Thompson, WHO's spokesman on communicable diseases, told journalists.
"This kind of reaction from local people is not uncommon in a haemorrhagic fever outbreak," he said. "They (locals) sometimes believe that it is the medicine people who have brought the illness to their communities."
The medics were following leads that up to 200 people could have come in contact with infected people, Thompson said.
So far, 14 health workers have died of the disease, he said.
''They (locals) sometimes believe that it is the medicine people who have brought the illness to their communities."
Uige residents needed to be better informed about the work of the surveillance teams, who have been collecting dead bodies and educating the public about the virus, another WHO official said.
The WHO has advised residents not to touch those infected with the virus or handle the bodies.
There is no cure for Marburg, first contracted by researchers in the German town of the same name from African monkeys. Marburg's monkey-to-human transmission is similar to the Ebola virus.
The previous worst recorded Marburg outbreak was during a 1998-2000 epidemic in the Democratic Republic of Congo, when 123 people died.