The boat that was running on the Chindwin river between Monywa and Homalin townships in the Sagaing region carried more than 250 passengers.
"It is confirmed that 48 bodies have been found (through) today, the rescue teams are still looking for missing bodies but we don't know how many exactly passengers were on the boat," local official Myo Nyunt Tun said, AP reported.
Authorities said 158 people were rescued and the teams of rescuers were searching for more bodies.
The cause of the capsizing was unclear but local police says the boat may have been overcrowded. A regional member of parliament said it is common that the ferry boats usually carry more passengers than they are allowed.
Kani Township police filed criminal charges against the helmsman alleging his negligence caused the deaths.
"The ferry boat was carrying more people than they were allowed, which is illegal, and that's why the police are taking action against the helmsman," said Tun Tun Win, a regional member of parliament.
Many people in Myanmar travel by boat, but poor maintenance and overcrowding makes the vessels prone to capsizing.
The local government said Wednesday it will take serious action against any overcrowded ferry boat in the region.