Chairman Peter Ridsdale has warned that Cardiff could consider quitting the FA of Wales for England after criticism from ex-FAW secretary Alun Evans.
Evans attacked the English FA's decision to allow Cardiff City to play in Europe if they win the FA Cup.
He went on to say that Cardiff had "no relevance" to Welsh football.
"What we need to do is spend this summer talking to the English FA about whether we should be fully affiliated to them," Ridsdale told BBC Wales.
"It's a disgrace suggesting that we're not doing anything for Welsh football.
"We supply a number of their players both at full international level and obviously in the Under-21s and further down the youth system.
"We are the capital of Wales and we are in the FA Cup final - we should be using that positively and not negatively."
The row was sparked by Thursday's decision by the FA to allow the Bluebirds to represent England in next season's Uefa Cup should they beat Portsmouth at Wembley on 17 May.
"People should be congratulating us on getting to an FA Cup final for the first time in 81 years," Ridsdale added.
"To start going to the press and saying we shouldn't be allowed in the Uefa Cup if we win it is beyond acceptability.
"The FAW have got their own plans which they seem to be sharing with nobody but themselves.
"Alun hasn't spoken to me about them, nor has anyone else at the FAW and we've played in the English league system now for almost 100 years.
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"Why shouldn't we get the same rewards as anybody else who wins one of their competitions."
The Uefa Cup decision is a U-turn on long-standing rules stating that the Welsh 'exile' clubs playing in the English league pyramid system can only qualify for European competitions via their own national tournaments.
That previously left the likes of Cardiff, Swansea, Wrexham, Newport County, Merthyr Tydfil and Colwyn Bay in an European limbo.
All those clubs are affiliated with the FAW but have chosen to play in competitions under the FA's umbrella.
Under Uefa rules clubs can only play in the competitions of one country.
However, European football's governing body was keen that Cardiff should be rewarded for their achievement should they win the FA Cup.
Meanwhile, Cardiff manager Dave Jones has welcomed the decision to allow the Bluebirds into the Uefa Cup if they beat Portsmouth.
"If we won the prize then rightly so," Jones said. "The question needed to be answered before the game rather than after it and now it's done.
"It's an unusual situation and now that we've got there [to the FA Cup final] the FA has answered it in the right way thankfully.
"Now we can look forward to winning it, that's the hard bit now.
"It's an added incentive to be able to go into Europe for the players, of course it is.
"But Cardiff City are in the FA Cup final and that only comes along once every 80-odd years and we'll be concentrating on the game, not whether we're going into Europe or not.
"Portsmouth will be looking at that as well and so what we've got to be is focussed, better than what we have been the past two games and now there's places up for grabs."
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