The Irish Football Association look certain to demand answers from FIFA after another youngster, Shane Duffy, decided he would rather play for Ireland.
Northern Ireland boss Nigel Worthington believes there could be flaws in a system that allows players who have come through the age groups with one nation to represent another country.
"There is a loophole, where a player can walk away after a lot of time and investment has gone in. Until it's resolved, that's where we are," Worthington told the BBC.
Worthington failed in his attempt to persuade promising Everton defender Duffy his long-term international future lies with the province.
Instead the 18-year-old has withdrawn from the squad to face Albania in a friendly on March 3.
Duffy's decision to switch allegiance to the Republic follows those of Manchester United midfielder Darron Gibson and Portsmouth defender Marc Wilson.
Wilson has been named in the Ireland squad for the first time as they prepare to meet Brazil.
Duffy progressed to the under-21 side after captaining the under-19s.
Worthington added: "Shane has represented Northern Ireland all the way through from a very early age to the under-21s.
"I am a big admirer of Shane. I like him as a player and a lot of work has gone in with different coaches. I am disappointed with the situation as he is going to be a very good player."