Iran Press/ Africa: The boat, which was carrying at least 80 people, capsized on Friday in the Ogbaru area in Anambra state.
Most of the victims were women and children, trying to reach safety after their community had been inundated by floodwater.
President Muhammadu Buhari offered his condolences to the families of the victims of the "tragic" accident.
He also ordered a review of safety measures across the country's water transport system and said emergency services must do everything to account for those missing.
Buhari called on government agencies "to check the safety protocols on these transport ferries to make sure such incidents are avoided in the future".
Local media reports say those aboard the boat were heading to the Nkwo market in Ogbakuba before it capsized. Some officials said the boat had suffered an engine failure and hit a bridge before capsizing.
Thickman Tanimu, the south-east coordinator of the National Emergency Management Agency, told the AFP news agency: "The water level is very high and too risky for a smooth search and rescue operation".
Anambra governor Charles Soludo added that the accident had been a shock both residents and the state's government, offering his sympathies to the victim's families.
Boat accidents are relatively common in Nigeria, although most are blamed on overloading or poor safety measures.
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