The man had been declared free of the deadly virus in Liberia last September, WHO spokesman Tarik Jasarevic told AFP.
"He has provided a semen sample which has tested... positive for Ebola, 175 days after his negative blood test," he said in an email.
The UN health agency had previously said the virus had been detected in semen around three months after a patient had been declared Ebola free.
"Ebola survivors should consider correct and consistent use of condoms for all sexual acts beyond three months until more information is available," it says on its website.
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Jasarevic said more research was needed before WHO could provide more detailed advice.
"We need to understand better if this particular case is an anomaly or if there really are groups of people who might (carry) parts of the Ebola virus longer," he said.
He said a number of studies were already under way, as well as discussions about whether Ebola survivors should be systematically screened after three months to determine their status.
"We should have answers to allow us to give more definitive advice to survivors very, very quickly," he said.
The deadliest outbreak of Ebola in history began in late 2013 and has killed more than 10,600 people, mainly in Liberia, Sierra Leone and Guinea.