Super Eagles players have also rejected the artificial turf, saying it hampered their play.
"We had a meeting with the players and they said they were not comfortable with the artifical turf," NFF executive committee member Christopher Green told KickOffNigeria.com.
Kick-off was delayed for 20 minutes as heavy traffic meant both teams could not get to the match venue on time, the players struggled on the artificial turf and the attitude of the fans in booing the home team and setting off fireworks further compounded the situation.
At least four players complained of the turf after the game, and NFF officials are also said to be unhappy about certain areas of the organisation, including what a top official described as the 'secretive' nature of part of the organisation.
Wednesday's friendly was marked as a dress rehearsal for the key qualifier, but officials now say that is no longer a certainty "No decision has been made yet, but the Ethiopia match may not be held in Lagos.
"The board will have to meet and decide on that," Green said.