NFF media manager Promise Efoghe said no reason was given for the decision to divert their plane to Al Abraq on Sunday.
“No Libyan FA official has come to give reasons or provide any clarification,” he said.
“The Libyans made no effort to help. When the NFF tried to make alternative arrangement, we were locked inside the airport.
“It’s like we are in a prison at the airport.”
Striker Victor Boniface said on social media that the squad were left without food, wi-fi or anywhere to sleep, and the Super Eagles account on X posted pictures of players sprawled out on airport chairs.
Troost-Ekong described their treatment as “mind games”, which the LFF denied.
“There are no grounds to accuse the Libyan security teams or the LFF of deliberately orchestrating this incident,” a statement added.
“Such actions are inconsistent with our values and principles.
“We firmly reject any claims that suggest foul play or sabotage in this situation.”
The journey from Al Abraq to Benghazi would take over three and a half hours by road, but Troost-Ekong said the players would not want to travel by that means because of the security situation in Libya.
The country is split between two administrations – one based in the eastern region, which includes Benghazi, and the other in the west in the capital Tripoli. Both governments claim to be the country’s legitimate rulers.
Efoghe said the Nigerian embassy in Tripoli was “handicapped” and could not intervene because of the political situation.
“We will not accept to travel anywhere by road here even with security. It’s not safe,” Troost-Ekong added.
“We can only imagine what the hotel or food would be like given to us if we continued.
“We respect ourselves and respect our opponents when they are our guests in Nigeria. Mistakes happen but these things on purpose have nothing to do with [international] football.”
Nigeria won 1-0 when the two sides met in Uyo on Friday and top Group D on seven points, with Libya bottom of the table on one point and on the brink of elimination.