Twenty bodies had been recovered by midday, Konna Mayor Sory Diakite told The Associated Press. At least 400 passengers were believed to have been onboard the vessel, though only 210 survivors had been counted, he said.
Family members in the capital of Bamako said they had received confirmation of the accident.
"The boat sank around 8 p.m. between Mopti and Konna," said Abouri Djittey, a resident of Bamako. "It was a survivor who called me around 9 p.m. to tell me that my 7-year-old daughter Ramata and her friend had both drowned."
The boat was traveling to the northern town of Timbuktu when it capsized Friday about seven kilometers (4 miles) from Konna, Diakite said.
"For the moment, the conditions of what exactly happened are not known," he said.
Crews were still searching the river for bodies late Saturday afternoon, said Ibrahim Maiga, who heads Radio Korondougou in Konna.
Large boats carry hundreds of people on the Niger River at this time of year, and the journey can take up to two nights and two days to reach the fabled northern town of Timbuktu. Boats are often overloaded, and some carry two levels of passengers.
While most Malians cannot swim, travel by water is preferable to journeying on the poor roads across the country's desert north.