Bolsonaro said Brazil will consider leaving the WHO unless it stops being a "partisan political organization."
Earlier, the WHO showed an opposite view against Bolsonaro's efforts to lift lockdowns, as the COVID-19 epidemic was still plaguing the country.
Replying to loosen the social distancing order, WHO spokeswoman Margaret Harris said a key criteria for lifting lockdowns should be slowing transmission.
With a new record of daily COVID-19 fatalities, Brazil outnumbered Italy to become a country with the third highest infections in the world.
Brazil' s total COVID-19 deaths have surged to 34,021 after its health ministry on Thursday reported 1,437 new deaths in the past 24 hours.
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