"We lost 18 lives. We were told there were about 70 people on the boat," Mohammed Shaba, head of the State Emergency Management Agency, told AFP.
The accident, which happened on Thursday, took place as people were returning from a weekly market, added the official.
Shaba said it was unclear whether overloading was to blame for the mid-river capsizing but said the vessel was "very old", like many of the boats operating that route.
The boat with an estimated 150 people on board "split" in two after setting off from Malilli village in Niger state.
The Niger is Africa's third longest river, after the Nile and the Congo, extending an estimated 4,200 kilometres (2,600 miles).
Waters on the river have risen sharply following a heavy rainy season in the area, which Shaba said could have been a contributing factor to last week's accident.