In a statement released last night, the FAI claimed the Association is the "first to recognise the extensive development programme of the IFA and congratulate them on their progress to date.
"The FAI acknowledge that this is a cross-community scheme and undertook to continue its policy of not approaching players born in Northern Ireland for the Republic of Ireland international teams.
Selection
"However, any player that opts to declare for the Republic of Ireland and notifies the FAI of this will be considered for selection."
The letter sent to Brian Lagan by the IFA's recently appointed community relations officer Shane Maguire asked the player if he felt his religion influenced his move.
Lagan claims he was overlooked by the IFA on three occasions.
Boyce admitted that the wording of the letter, exposed on the same day the IFA received a FIFA Fair Play accolade, caused "embarrassment.''
"We admit that it was somewhat naive to have mentioned religion in the letter to Brian Lagan. But I want to stress that there was nothing malicious in the wording.
"Of course we want to know why the player made the move but I will deeply contest anyone who suggests that we (the IFA) are not concerned with religion or politics.
"I would be offended if any player was to accuse me or the association of having a sectarian policy.''
Next season the FAI National League champions and cup winners, will compete in a tournament with the Irish League champions and Irish Cup winners.
Arrangements for the Omagh Trust Fund international at Lansdowne Road on May 29 between Northern Ireland and the Republic were confirmed.
The FAI will allocate an initial 3,400 tickets for distribution through the IFA for the fixture.
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