Responding to a call from more than 100 leading scientists, who said it would be unethical for the Games to go ahead as scheduled, the United Nations health agency said having the Games in Rio as planned would "not significantly alter" the spread of Zika, which is linked to serious birth defects.
"Based on the current assessment of Zika virus circulating in almost 60 countries globally and 39 in the Americas, there is no public health justification for postponing or cancelling the games," the WHO said in a statement.
In a public letter posted online on May 27, around 150 leading public health experts, many of them bioethicists, said the risk of infection from the Zika virus was too high for the Games to go ahead safely.
The letter, sent to WHO director-general Margaret Chan, said the Games, due to be held in Rio de Janeiro in August, should be moved to another location or delayed.
"An unnecessary risk is posed when 500,000 foreign tourists from all countries attend the Games, potentially acquire that strain, and return home to places where it can become endemic," the letter said.
But the WHO rejected the call, saying Brazil "is one of almost 60 countries and territories" where Zika has been detected and that people continued to travel between these countries and territories for a variety of reasons.
"The best way to reduce risk of disease is to follow public health travel advice," it said.
One of the signatories of the letter, brain injury specialist Dr Ford Vox, called the WHO's response "defeatist, depressing, and quite a bit too quick for anyone to believe they gave the letter due consideration."
The scientific community is divided over the threat of Zika due to the Rio Olympics, with many experts saying the call for postponement or relocation is unjustified.
"We live in an incredibly interconnected world, global travel and trade are daily activities that offer Zika virus an opportunity to spread," said Jonathan Ball, professor of molecular virology at the UK's University of Nottingham.
"By comparison to these routine activities, the increased risk that the Olympics poses is a drop in the ocean."
The WHO's advice is that pregnant women should not travel to areas with Zika virus transmission, including Rio de Janeiro. It also advises everyone to make all efforts to protect against mosquito bites and to practice safe sex.
Zika infection in pregnant women has been shown to be a cause of the birth defect microcephaly and other serious brain abnormalities in babies.
The connection between Zika and microcephaly first came to light last fall in Brazil, which has confirmed more than 1,400 cases of microcephaly.
The International Olympic Committee jumped into the debate by saying the WHO's response was not made in consultation with the Olympic body. It also denied there was a "secret" memorandum of understanding between the WHO and IOC.
"The IOC does not currently have a Memorandum of Understanding with the World Health Organisation," a spokesman said.
The IOC has said it was monitoring the development of Zika through the WHO for up-to-date information and guidance but has repeatedly said the virus would not pose a threat to the Games.