Spokesman Ibrahim Farinloye of the National Emergency Management Agency told The Associated Press the ferry was carrying traders to a weekly market at Malali village when the storm erupted Friday afternoon.
He said Saturday that it was impossible to say how many people died or were on the boat. But he said initial indications were that 42 had drowned and about 200 passengers were missing.
The official News Agency of Nigeria reported 15 bodies had been recovered and buried alongside the river.
Nigeria's rainy season often brings violent storms that can cause disasters in a country where there is little maintenance and corruption blights the construction of everything from buildings and boats to roads and dams.