The accident occurred about 2 p.m. Friday near the village of Malilli in the Borgu local government area, the Nigerian Bulletin reported.
Malam Ibrahim Hussaini, the public relations officer for the Niger State Emergency Management Agency, told the News Agency of Nigeria that the boat had been loaded with more than 150 passengers when it capsized halfway between Malili and Tungo Illo.
Hussaini said local divers had recovered 42 bodies, but about 100 people were unaccounted for.
"We believe that the boat was overload because the boat's capacity was put at 60 passengers, but over 150 passengers were said to be on board during the incident," State Government Secretary Alhaji Saidu Ndako said.
"The debris in the swollen river may also have been responsible for the incident."