"From the point of view of mobility, the situation is better than yesterday," Eduardo Paes, the mayor of Rio de Janeiro, said.
"The city is starting to return to normal, but the rains are still intense."
'Lives at risk'
Paes called on those living in hillside slums at risk for mudslides to leave their homes as the rains continued.
"Their lives are at risk," he said.
Luiz Inacio Lula da Silva, the president, said that decades of administrative misconduct had allowed inadequate home construction in the high-risk zones slum areas.
He said that Rio de Janeiro city authorities had ignored substandard construction for too long, even on the landslide-prone surrounding hills.
Lula vowed that his government would work to improve the quality of construction in these areas.
Al Jazeera's Craig Mauro, in Rio de Janiero, said: "For the people here in the slums this was not a surprise it happens every year. Not on this scale, but every year.
"And the thousands of people who live here are angry."
Mauro said that city officials had defended themselves, having said that no city could have coped with the amount of rain that has struck Rio de Janiero in the past few days.
Torrential rains began early evening on Monday, before a lull on Tuesday and then intensification after sunset that day.
Officials have voiced fears that flooding could worsen on Wednesday, and that continuing rains may dislodge saturated ground leading to more mudslides.
"All the major streets of the city are closed because of the floods, each and every person who attempts to enter them will be at enormous risk," Paes said.
Schools were suspended for a second day on Wednesday, while a football match for major local club Flamengo was cancelled.
The latest flooding and transportation chaos has renewed attention on Rio de Janeiro's poor infrastructure as it prepares to host the football world cup in 2014 and the Olympic Games in 2016.