The African champions were required to travel by road following the postponement of their flight as they needed to catch a connecting flight to Abuja
Nigeria's senior women national team had to return to Lagos by road from Cotonou on Tuesday after the airline postponed their flight.
The team lost their bid to grab a ticket to the 2016 Olympic Games after losing 3-2 on aggregate to Equatorial Guinea on Sunday.
A 2-1 defeat after extra time to the Nzalang Nacional at Estadio de Bata ensured the African champions suffered their first defeat on the continent in 36 months.
The team flew to Bata from Lagos via Cotonou last Thursday, but upon their return were condemned to travel by road after being left stranded in Benin Republic by the airline.
Sources claim the team was abandoned for hours in Cotonou, before connecting by road to Lagos.
However, NFF spokesman Ademola Olajire said the action was taken owing to flight delays.
"It was the decision of the team officials to travel by road after their flight from Cotonou to Lagos was postponed indiscriminately,” Olajire told Goal.
"In order not to miss their flight from Lagos to Abuja, they decided to travel by road since the distance between Cotonou and Lagos was just one-and-a-half-hours.
"How did they fly from Equatorial Guinea to Cotonou if they never had a return ticket? They won't have traveled by road after flying from Bata to Cotonou with no flight delays.
"Their flight from Cotonou to Lagos which was initially scheduled for 1pm was postponed to 5:30pm and they had a connecting flight from Lagos to Abuja scheduled for 5pm.
"So the officials resolved to return by road - doing this means funds for their return ticket have been wasted all in the bid to avoid missing their flight to Abuja," he concluded.
The team was received on arrival in Abuja by NFF 1st vice president Barrister Seyi Akinwunmi.
Interim coach Chris Danjuma has announced a week's break for the team before re-grouping for preparations for the 11th All Africa Games in Congo-Brazzaville early next month.