The National Emergency Management Agency (Nema) says heavy rains caused the Niger River and Benue River to overflow.
It has resulted in a series of floods across the country over two weeks, with rural areas most vulnerable.
The government is urging residents along waterways to relocate to safe places.
Thousands of people have been displaced and vast swathes of farmlands have been destroyed by the floods in central and southern Nigeria, says the BBC's Is'haq Khalid in the capital, Abuja.
Worst hit is Niger State, where more than 40 people have died, Nema director Mustapha Yunusa Maihaja told the BBC.
Eleven other states have been affected - they are Kwara, Benue, Kogi, Adamawa, Taraba, Kebbi, Bayelsa, Edo, Anambra, Rivers and Delta.
Nigerian authorities are considering declaring a state of emergency, saying more floods could hit in the coming days and weeks as heavy rains continue.
Nigeria faces flooding almost every year.
Analysts blame recurring flood disasters on lack of proper town planning, blocked waterways and poor drainage systems.
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