World governing body Fifa has suggested that players born in Northern Ireland should be allowed to opt to play for the Republic of Ireland.
Howard Wells is amazed by the Fifa proposals
Fifa's legal committee wrote to Irish FA officials in the north and their FAI counterparts in the Republic outlining their view on the long-running dispute.
IFA chief executive Howard Wells says he is "staggered" by the decision.
"This proposal seems to be totally inconsistent with Fifa's own rules and we will be seeking clarification."
Wells told the BBC that the Fifa proposal was "totally inconsistent with the body's own rules which apply to the other 206 countries in the organisation".
"I am extremely surprised about this, to say the least. In fact I am staggered.
"All we are asking is for Fifa to apply their own rules consistently to all members of their organisation.
"This proposal flies in the face of what was said to us just a few weeks ago at a meeting in Zurich."
Wells hinted that the IFA would be taking legal advice before further pursuing the matter.
The IFA had expected Fifa to back its argument that players born in the north should turn out for Northern Ireland.
Fifa said it had asked for feedback from the two associations.
It added that any final decision on the matter would have to be approved by Fifa's executive committee.
The FAI has welcomed the latest stance from Fifa.
"We are pleased that Fifa has once again upheld the principle that players born in Northern Ireland should be free to choose whether they wish to play for the Republic of Ireland or Northern Ireland," said an FAI statement.
"The FAI will now meet with its legal advisors to review in detail the proposals contained in the Fifa letter before formulating a response."
On-loan Wolves midfielder Darron Gibson recently played for the Republic in a Euro 2008 qualifier.
He was born in Londonderry in Northern Ireland but elected to switch to the Republic after representing the north at Under-16 level.