As many as 27 people were confirmed dead in Espirito Santo and 18 in Minas Gerais, according to the latest Civil Defense report.
More than 60,000 people were forced to leave their homes due to widespread flooding and landslides in Espirito Santo, where 52 of the states 78 towns declared a state of emergency. In Minas Gerais, 25 towns declared a state of emergency.
In a radio interview on Wednesday, Espirito Santo State Governor Renato Casagrande said the days-long storm was the biggest natural disaster in the history of the state.
Minas Gerais had yet to appeal for federal aid, while a contingent of relief workers composed of army troops, firefighters and the National Security Force was dispatched to Espirito Santo after local authorities requested federal help with search and rescue efforts.
The Fire Force was also helping rescue people from remote and isolated locations.
The Brazilian Health Ministry was planning to send more helicopters, ambulances, relief workers and medicine to the disaster-hit areas.
Earlier in the day, the government published a presidential decree to facilitate the flow of federal aid to disaster zones by cutting down on red tape.
Rainstorms are common in the summer season of southern Brazil. A deadly storm in Rio de Janeiro state claimed more than 900 lives in January 2011.