"Yes, he has agreed to play for Nigeria," NFF president Amaju Pinnick told ESPN.
"His documents have been sent to FIFA since."
Ejaria, 22, was born in England to Nigerian parents, and he trained with the Nigeria cadet team in 2013 before accepting a call up to represent England at under-20 level.
Nigeria coach Gernot Rohr referred questions about Ejara's change of allegiance to the NFF, but a team source told ESPN that the player's documentation had been delayed because of the coronavirus lockdown and would probably need to be re-filed
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Nigeria international Ogenyi Onazi speaks about the fears from Turkish league players to return to training.
"The boy has agreed, but the papers are not approved yet by FIFA," the source said.
"There is still a process to it.
"We might need to resubmit because by the time coronavirus lockdown is over; the initial application might be dated.
"Plus he needs to do a fresh Nigerian passport, which he hasn't been able to do as yet."
Ejaria, currently on loan at Reading in the English Championship, becomes the latest in an army of players born and raised outside Nigeria who will wear the Super Eagles' colours at senior level. Currently, those players make up nearly half of Nigeria's starting XI.