Wilkinson, the Football Association's technical director, has even been accused of cheating fans by Peter Ridsdale, the chairman of Leeds United - the club he used to manage.
The World Under-20 Championship is taking place in Nigeria in April, and potentially Wilkinson could have a strong England side at his disposal, with Aston Villa's Gareth Barry, Joe Cole of West Ham and even Michael Owen eligible for selection.
As a full international, Owen is not likely to be included for the three- week tournament, which runs from 3 to 24 April. However, Wilkinson is eager to name the strongest possible squad - and Leeds look set to be particularly hard hit.
The defender Jonathon Woodgate, the striker Alan Smith and the goalkeeper Paul Robinson have all been integral parts of the first-team plans of the Leeds manager, David O'Leary, this season - but the Elland Road club could be deprived of all three. The situation has prompted an angry response from Ridsdale, who believes that, although the tournament is a worthwhile event, young players currently experiencing life in the first team would benefit more by staying in England.
"It is very important that players of 18 and 19 who are not in the first team should get as much experience as possible and they can get that through playing in this tournament," he said. "But I think that players who have emerged into firstteam football in the Premiership shouldn't be taken away at a time when your whole season is being determined.
"Championships, FA Cups and European places are being determined and if Howard Wilkinson takes these players then he is cheating the fans, who have paid their season ticket money, and putting the future of individual clubs at risk."
Any player selected for the competition would miss five scheduled Premiership matches, plus the possibility of an FA Cup semi-final and replay. The likes of Wes Brown from Manchester United could also be forced to sit out a European Cup semi-final.
An already unattractive dilemma for Wilkinson became even worse with yesterday's news that the World Under-18 Championship qualifying tournament - postponed in Israel in November because of the political situation in the Middle East - will now take place in March. From 7 to 14 March, England will compete against the new host nation, Spain, Andorra and Israel - and if they go through they will have to play a two-legged play-off on 31 March and 28 April. Woodgate would also be a prime candidate for that competition as well.
The Leeds manager has left Wilkinson in no doubt where his priorities should lie. "I am prepared to fight this all the way," O'Leary said. "We are striving to qualify for Europe again, so if we were to lose so many of our players it would be a joke.
"As well as being potentially damaging, those players are regularly involved with the first team and hopefully will be challenging for honours with us in April," the Irishman added. "What do the FA think these players will learn in Nigeria? There is no comparison to playing in the Premiership."
In contrast to Leeds, Liverpool have had some good news with regard to an international tournament. It was believed that Cameroon would require the defender Rigobert Song on 24 January, when the Anfield side face a fourth-round FA Cup tie at Old Trafford against Manchester United.
However, the 22-year-old Song, who has agreed a pounds 2.8m move from the Italian Serie A club Salernitana and is now waiting for the Department of Employment to issue a work permit, has to serve a two-match international ban and is unable to play for Cameroon in their African Nations' Cup fixture that weekend.