The storm on Friday caused torrential rains and helicopter searches are under way in flooded neighbourhoods to find 20 others who have gone missing, the government of Rio Grande do Sul said in a press release.
One of the worst hit on the cyclone's trail was the town of Caraa, with a population of more than 8000 people.
"The situation in Caraa deeply worries us. It is essential that we can, in an organised way, quickly map the main affected areas and identify the people who need support," said Rio Grande do Sul's governor, Eduardo Leite, who visited the area.
As of Friday night, Maquine, a municipality on the eastern coast, had received around a foot of rain, authorities said.
Many residents in affected areas have taken shelter in outdoor sports facilities in their towns. The authorities have issued a warning for a risk of landslides in several areas.
Leite said authorities have carried out 2400 rescues in the past two days.
"Our main objective at this first moment is to protect and save human lives. We are rescuing people who are stranded, locating missing people and giving all the support to the families," he said.
Deadly flooding in Brazil is common and has caused devastation for decades.
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