The M.V. Miraj-4 ferry capsized and sank in high winds and rain on the Meghna river on Thursday. The accident occurred in Munshiganj district, around 50 kilometers (30 miles) south of the capital Dhaka.
More than 200 people were believed to have been aboard the vessel when it sank. At least 12 people were killed, officials said.
Rescue ships were called in and divers from firefighting and civil defense departments dispatched to search for the missing.
"We fear there will be more bodies inside the vessel and we cannot be sure of the number of passengers [on board]," Deputy Commissioner of the Munshiganj district Saiful Hassan Badal told Reuters by telephone from the scene of the accident.
The ferry was traveling to the southern district of Shariatpur from Dhaka when it experienced problems during the storm. Some survivors were able to swim ashore, despite strong currents and high waves.
Bangladesh has a history of deadly ferry disasters. Casualties have sometimes extended into the hundreds. Some 150 people were killed in March 2012 when a ferry carrying 200 people was struck by an oil barge and sank.
At least 85 people were killed in 2009 when an overloaded ferry capzsized off Bhola Island in the south of Bangladesh.
dr/ipj (AFP, Reuters, dpa)