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More than 2,600 people have been forced to flee their homes, the agency added.
The rains have caused blackouts, landslides, washed-out roads and collapsed bridges across the state.
Many of the areas affected were damaged during the floods in May last year, which killed more than 100 people and prompted promises to take measures to avoid a repeat of the dramatic events.
“The state is better prepared,” Governor Eduardo Leite said Wednesday on X platform, pointing to strengthened response teams and investments in river dredging to reduce the risk of flooding.
Leite added that some regions had received over 350 millimetres of rain since the weekend.