Fifa have described a ruling from the Court of Arbitration for Sport allowing clubs to pull their players out of the Olympics as "disappointing" and urged clubs to allow their players to compete in Beijing.
CAS today ruled in favour of Barcelona, Werder Bremen and Schalke, stating that clubs could not be forced to release their players as the Olympics do not appear on FIFA's calendar.
Fifa had insisted that it was "mandatory" for clubs to release players aged 23 and under for the tournament.
In a statement, Fifa said it would respect the CAS ruling.
"Fifa is surprised and disappointed by this decision, but we respect it," Fifa president Sepp Blatter said.
"Nevertheless, I appeal to the clubs: Let your players take part in the Olympic Games! It would be an act of solidarity in perfect harmony with the Olympic spirit. It would be wonderful for the players, for the fans and for the game itself."
CAS found that Fifa's position was based on custom rather than law, meaning clubs could not be forced to release their players.
"The Olympic Football Tournament Beijing 2008 is not included in the Co-ordinated Match Calendar and there is no specific decision of the Fifa Executive Committee establishing the obligation for the clubs to release players under 23 for this tournament," the CAS ruling said.
"The requirements to justify a legal obligation of clubs to release their players for the Football Tournament Beijing 2008 on the basis of customary law are not met."
Blatter added that he had made a direct appeal to the clubs involved to allow the three players at the heart of the dispute - Barca's Argentinian playmaker Lionel Messi, Schalke's Brazilian defender Rafinha, and Werder Bremen's Brazil midfielder Diego - to compete.
The three clubs made the appeal as they do not want the players to miss the start of the season. The Bundesliga season in Germany begins before the conclusion of the Olympics and Schalke will also play a Champions League qualifier.
Barcelona will have also have a Champions League qualifier to play before the Olympics conclude.
While the CAS ruling overturns the decision delivered by a Fifa-appointed judge last week, Blatter insisted that Fifa's position has not changed.
"The Olympic Football Tournaments are a unique opportunity for a player as they are high-level competitions that give everyone involved - most notably young players - the chance to gain international experience that will stand them in good stead for the future," he said.
"It stands to reason, therefore, that it is not only the player and his national team who can benefit from such an experience, but also his club.
"I regret that the CAS has not taken the Olympic spirit into consideration."
While the three clubs who made the appeal can be expected to pull their players out, it appears unlikely that any others will be withdrawn as they have travelled with the permission of their clubs with many such as Belgium's Vincent Kompany cutting deals to allow them to play.
Fifa's statement concluded: "Fifa wishes to thank all those clubs who have released their players for the competition and shown great solidarity and Olympic spirit in doing so."
In its statement, CAS stated that it hoped the decision would not cause major disruption to the tournament.
"In view of Fifa's recommendation made to the clubs to release their players as well as of the Olympic spirit, the CAS call upon the good will and good sense of Fifa and the clubs to find a reasonable solution with regard to players who wish to represent their country in the Olympic Games," the statement said.
The format of the Olympic tournament is now expected to be reviewed before the 2012 Olympics in London.
Fifa said it would meet with the International Olympic Committee after the conclusion of the Beijing Games to clarify the issue for the future.