Jatto Asihu Abdulqudir, 36, a protocol assistant, was travelling to an Ecowas function with Liberian Patrick Sawyer, the man who brought Ebola to Nigeria last month.
Mr Abdulqudir had been under quarantine and Nigeria has reported eight cases of Ebola since Mr Sawyer arrived on July 20.
Ecowas said in a statement: "The Commission wishes to reassure staff of all community institutions all over the entire region that it is taking all necessary steps to guarantee their health and safety."
The death came as Guinea Bissau decided to close its frontier with eastern neighbour Guinea in a bid to prevent the entry of the deadly Ebola virus in a move announced by Prime Minister Domingos Simoes Pereira.
The disease has killed more than 1,000 people in Guinea, Liberia and Sierra Leone in the world's worst outbreak of Ebola, and the World Health Organisation has called it an international emergency.
Germany, meanwhile, has urged its nationals to leave Liberia, Guinea and Sierra Leone due to concern over the Ebola virus.
The request did not apply to medical workers or German diplomatic staff and embassies will remain open, the foreign ministry said.