The union represented more than one million Brazilian doctors who sent the files, calling on the International Criminal Court to investigate how the Bolsonaro government responded to Covid-19.
"President Jair Bolsonaro's government has committed negligent crimes in dealing with the Covid-19 pandemic, threatening the lives of health workers and the people of Brazil. We believe this is the first lawsuit against a government.
Marcio Monzane, UNI Americas union representative, the organization leading the lawsuit, said the Bolsonaro government was responsible for "the merciless response to the pandemic".
The ICC was founded in 2002 to deal with cases involving war crimes, genocide and crimes against humanity.
Brazil is the second-largest Covid-19 epidemic region in the world with more than 2.4 million people infected with nCoV, of which more than 87,000 have died, the second most in the world, behind only the United States.
Bolsonaro repeatedly underestimated the threat of an epidemic, calling it a "pimple flu" and ignoring the rules and measures to isolate the community, including wearing masks in public places.
As of last week, Brazil spent two months without a health minister after Nelson Teich resigned to protest Bolsonaro in favor of using hydroxychloroquine and chloroquine to treat Covid-19.