NFF media manager Promise Efoghe said no reason was given for the decision to divert their plane to Al Abraq.
“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.”
Nigeria 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 seating.
Troost-Ekong announced the intention to boycott the match during a series of posts on Monday morning.
“As the captain together with the team we have decided that we will not play this game,” the centre-back said.
“I’ve experienced stuff before playing away in Africa but this is disgraceful behaviour.”
In response, the LFF said that disruptions can occur from routine air traffic protocols, security checks or other logistical challenges and said it hoped the misunderstanding “can be resolved with understanding and goodwill”.
Senator Enoh said he had held talks with Caf president Patrice Motsepe and secretary general Veron Mosengo-Omba, and that African football’s governing body wanted the match to go ahead as scheduled at 19:00 GMT on Tuesday.
“There must be a serious adverse consequence to the LFF for this unspeakable behaviour,” Enoh said in a statement.
“This cannot be through insisting that Nigeria still takes part in this match given the very obvious situation.
“The team insists they’re unable to go ahead with the match, not just because of the trauma and consequent psychological torture but also because of fear for their safety.”