The 52-year-old male doctor was found dead in a hotel room in what the local police said was a suicide, a ministry spokesman said. The ministry did not release the name of the doctor or more details about the death.
He was one of more than 7,000 Cubans who are in Brazil as part of a program that hires foreign doctors to tend the sick in slums and remote rural locations where there are no Brazilian physicians.
Since its start last year the "More Doctors" program has been roiled with controversy as some Brazilian physicians tried to bar the entry of Cuban doctors who they said threaten to undermine the country's medical standards.
The defection of a Cuban doctor over low pay in February also raised complaints by some opposition politicians who said the physicians were being exploited.