The accident took place on Thursday at the town of Diré, officials said on Tuesday.
Local authorities had not yet released an official death toll, but regional resident and former National Assembly deputy Alkaidi Touré said Tuesday that 38 were killed and 23 survived.
Diré resident Moussa Ag Almoubarek Traoré said he lost 21 family member in the accident, and that he helped retrieve and tally the dead with local officials.
"I collected the bodies that were scattered across the river, and some were already decomposing. As I speak to you now, I can still smell the bodies," Traoré tole the Associated Press.
The boat was carrying families and farmers who had just harvested rice, witnesses said, arriving after nightfall when docking is banned due to security measures aimed at thwarting attacks by al Qaeda-linked militants in the region. But Traoré said the boat driver didn't want to wait until morning and tried to come ashore in another location, where the boat hit rocks and sank.
Mali, a country of 25 million people, has battled jihadi militants for several decades, alongside neighbouring Burkina Faso and Niger. Militants from the al-Qaeda-backed Jama'at Nusrat al-Islam wal-Muslimin (JNIM) group are active in the Timbuktu region of Mali.
Accidents involving ferry boats on the Niger River are not uncommon, and although there are no reliable statistics on this type of accident, the human toll of this accident is unusually high.
"The entire region of Timbuktu is in mourning, because this accident has had a profound impact on the population, as many women and children drowned," Alkaidi Touré said.
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