Cardiff City and Swansea City have been warned they cannot leave the Football Association of Wales' governance.
Cardiff and Swansea chairmen have held talks with the Football League about the possibility of a switch to come under English administration.
Bluebirds chief Peter Ridsdale and Swans chairman Huw Jenkins have had talks with Football League boss Lord Mawhinney in London.
But FAW chief David Collins has said: "I don't think they can leave the FAW."
Cardiff and Swansea are two of the six Welsh clubs that play in the English pyramid system but have always been ruled by the Welsh FA rather than England's Football Association.
Now the two Championship high-fliers are exploring the possibility of whether they can leave the FAW to be administered by The FA.
The Bluebirds were told before last season's FA Cup final - where Dave Jones' team have a chance of qualifying for Europe - they will not be entered for the Uefa Cup if they did beat Portsmouth because they were not an English club.
Ridsdale has revealed that Lord Mawhinney invited him and Jenkins to a meeting to discuss the possibility of leaving the jurisdiction of the Football Association of Wales.
"I did accept an invitation for talks in London with Lord Mawhinney and Huw Jenkins also attended the meeting," he told the Western Mail newspaper.
"But we cannot and will not initiate anything. We are in Wales and part of the Football Association of Wales.
"However, Premier League chairman David Richards has made it clear he feels we should be in the Football Association if we are promoted."
The Welsh FA deal with the disciplinary matters of Cardiff and Swansea as well as of the issues of non-league clubs Wrexham, Newport County, Merthyr Tydfil and Colwyn Bay.
And the FAW also look after player registration and transfers, hence why players transferring between English and Welsh clubs require international clearance despite the two clubs being in the same league pyramid.
Since Wales' English league teams stopped competing in the Welsh Cup in 1995, those breakaway six have had fewer dealings with their governing body.
But FAW secretary general Collins, a long standing committee member at European football's governing body Uefa, said he could not see how Cardiff or Swansea could leave their home association.
"They are a native of Wales so I cannot see how they can leave the Football Association of Wales," Collins told BBC Sport.
"Every club in every European country is a subject of their home association and every association is a subject to Uefa so Cardiff and Swansea would have to get special dispensation."
The disciplinary situation infuriated the then Portsmouth manager Harry Redknapp before last season's FA Cup final after the FA of Wales overturned captain Darren Purse's cup final ban.
The Ninian Park club had appealed against Purse' three-match suspension following his straight red card after a clash with Andy Cole in Cardiff's 3-3 draw with Burnley.
At the time, Pompey boss Redknapp said: "Cardiff play in the English league, in the English cup and want to represent England in the Uefa Cup - and when they get a player sent off it goes before the Welsh FA.
"How can that be right?
"I don't want to see the boy miss the cup final - but Andy Cole said it was the worst challenge that he has ever received."
Collins insists Cardiff and Swansea potentially leaving the FAW has not been discussed by the FAW's full committee.
The clubs could ultimately consider legal action if they wanted to challenge the status quo.