Trials in several countries are being “temporarily” suspended as a precaution, the agency said on Monday.
It comes after a recent medical study suggested the drug could increase the risk of patients dying from Covid-19.
President Donald Trump has said he is taking the drug to ward off the virus.
The US president has repeatedly promoted the anti-malarial drug, against medical advice and despite warnings from public health officials that it could cause heart problems.
Last week, a study in medical journal The Lancet said there were no benefits to treating coronavirus patients with hydroxychloroquine, and that taking it might even increase the number of deaths among those in hospital with the disease.
Hydroxychloroquine is safe for malaria, and conditions like lupus or arthritis, but no clinical trials have recommended its use for treating Covid-19.
The WHO, which is running clinical trials of various drugs to assess which might be beneficial in treating the disease, has previously raised concerns over reports of individuals self-medicating and causing themselves serious harm.
On Monday, officials at the UN health agency said hydroxychloroquine would be removed from those trials pending a safety assessment.
The Lancet study involved 96,000 coronavirus patients, nearly 15,000 of whom were given hydroxychloroquine – or a related form chloroquine – either alone or with an antibiotic.
The study found that the patients were more likely to die in hospital and develop heart rhythm complications than other Covid patients in a comparison group.
The death rates of the treated groups were: hydroxychloroquine 18%; chloroquine 16.4%; control group 9%. Those treated with hydroxychloroquine or chloroquine in combination with antibiotics had an even higher death rate.
The researchers warned that hydroxychloroquine should not be used outside of clinical trials.