The accident happened near Gorau in Goronyo local government area and rescue efforts are continuing, said Abdulkadir Yusuf, an area manager at the National Inland Waterways Authority.
A Reuters witness saw 50 bodies, many wrapped in mats and traditional cloths, lying in the forecourt of a community mosque ahead of their burial in Gorau later on Thursday.
Deadly boat accidents are relatively common in Nigeria, where overcrowding, poor maintenance and weak enforcement of safety regulations often contribute to disasters on the country's rivers and waterways, particularly during the rainy season.
One local resident said the boat had been carrying farm owners and labourers hired to harvest rice and that more than 70 people had been onboard when it capsized.
Another resident said there were 57 people on board.
Yusuf said the bodies of about 40 children had been found.
Nasiru Adamu, an MP at the Sokoto state legislature from the area, said that those onboard were mostly aged between 10 and 15 years old, adding that 16 people had been rescued.
"We have buried 46 people, and even more dead bodies have just been brought. The death toll is 53," said Sharhabilu Kiliya, one eyewitness.
Mustapha Umar, director of relief and rehabilitation at the state's emergency management agency, said officials were heading to the scene and would provide further information later.
In January, at least 25 people died when a leaking boat capsized in Yobe state, northeast Nigeria.
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