The Togo team were at the airport in Lome on Monday ready for the 400-mile flight when Adebayor asked them not to board, claiming there were rumours the plane would crash.
He managed to frighten his team-mates sufficiently that the flight was delayed 24 hours, and his condition for making the trip the following day was that Togo FA president, Tata Avlessi Adagio de Mass, should fly with the team.
Adebayor said: "My life is very dear to me and, if we have to go down, we'll all go down together with the president.
"There are rumours that, if we get on, the aircraft will go down."
However, when the Federation president said he would not make the flight due to a family bereavement, Adebayor refused to fly at all, leaving the rest of the squad to depart without him.
Adebayor's fear is thought to stem from an accident last year when several Togo officials were killed after their helicopter exploded attempting to land.