Marcondes says most died at sea and their carcasses washed ashore. Some beached while still alive and perished.
Marcondes said Wednesday that the deaths reflect a higher mortality rate.
Scientists are investigating whether disease may be a factor, or if warming oceans may be diminishing the supply of krill that whales eat.
Humpbacks travel from Antarctica to warmer Brazilian waters to reproduce between July and November.
Seven non-humpback whales have also been found dead this year.