The country was declared free of the virus a year ago.
Ten people were quarantined after coming into contact with the man, who was said to have shown Ebola-like symptoms.
A WHO spokesman later confirmed the man had tested negative for Ebola and Lassa fever.
He died shortly after being admitted to hospital in Calabar, officials said.
On Wednesday, the three countries worst affected by Ebola - Guinea, Sierra Leone and Liberia - recorded their first week with no new cases since the outbreak began in March 2014.
More than 11,000 people died in the West African Ebola outbreak, the worst known occurrence of the disease in history.
New cases have fallen sharply in 2015, but the WHO has warned that the disease could break out again.
The latest scare happened when a patient arrived at the University of Calabar Teaching Hospital on Wednesday.
Those quarantined included nurses who had attended to the patient, said Queeneth Kalu, the hospital's chief medical director.
Ebola arrived in Nigeria in July 2014 when a Liberian businessman collapsed at Lagos airport.
But the outbreak was contained with seven deaths - far fewer cases than in the worst-hit countries.
A man who died in southern Nigeria in a suspected case of Ebola did not have the deadly virus, the World Health Organization (WHO) has said.