The double-decker ferry, MV Lighting Sun, was sailing to Dhaka on the Meghna river from the southern Madaripur area when it was swamped by a sudden storm near Chandpur, 170km from the capital.
First reports available with police said eight bodies, including women and children, had been found.
They said villagers and fishermen using motor boats picked up at least 35 survivors. Another five were retrieved alive from atop the hull of the upturned ferry, which was floating partly submerged in the river.
"The ferry sank in the Meghna's midstream, off the Anandabazar fishing centre, at about 3:30am. The river is very turbulent with strong winds still blowing," said a
reporter at the scene.
About 400 people were killed and hundreds remain missing after a triple-decker ferry sank in a storm, also in Chandpur district, in July last year.
Impoverished and over-populated Bangladesh has a long history of ferry disasters.
Inland water transport authority officials say about 1000 people die in ferry accidents in the country on average every year, but the number of missing is far more.
Bangladesh is struggling to clean up one of the world's deadliest ferry industries before the annual rainy season next month, when hundreds are killed every year in shipping disasters on the country's turbulent rivers.
The government has banned night sailing by small ferries and issued warnings to owners of larger vessels not to take on excess cargo and passengers. Listening to weather bulletins is also now mandatory for sailors.
"We are taking extra precautions in the months of May and June - preceding the rainy season - when powerful storms often strike," shipping minister Akbar Husayn said in an interview on Friday.
"We are taking extra precautions in the months of May and June - preceding the rainy season - when powerful storms often strike"
"Safer berths are also being planned at vulnerable sites for sheltering ships during storms," he said.
Low-lying Bangladesh is laced by thousands of kilometres of waterways that are crucial trade and travel routes for the congested country's 140 million people.
Only a few major bridges provide transport across the several large rivers that bisect the country.
Every wet season, the waterways become menacing torrents and the country is frequently lashed by cyclones that sweep in from the Bay of Bengal.
Lax safety standards, poorly maintained vessels, corrupt officials and unscrupulous owners competing with other operators to make a profit, largely contribute to the problem.