Barcelona president Josep Maria Bartomeu believes FIFA regulations concerning under-age player transfers needs to be revised and that current rules would have prevented Lionel Messi from joining the club.
Now Real Madrid are also being investigated by FIFA over the transfer of 51 players and there are rumours that the activities of other La Liga clubs could be examined.
The ban is a major blow for Barca, who have been held up as an example for their development of youth players through their celebrated Masia academy, where they nurtured the talent of Argentine-born Messi after he arrived at the club aged 13.
Bartomeu is angry at the way they have been treated.
"The problem is with FIFA and they need to change this article 19 (over the transfer of youth players) as it doesn't make any sense," the president told Spanish radio.
"Leo Messi couldn't have come to Barca according to FIFA. FIFA have a problem and they can't have a rule which so many kids are not complying with. At the moment, it is Barca who are paying for five kids.
"Barca have suffered injustices in the past and this is another example.
"Clearly there are going to be other clubs involved, (Spanish federation president Angel Maria) Villar already told us that other Spanish teams were being investigated.
"I don't want other clubs to be investigated. I want FIFA to change the rules and (FIFA President Sepp) Blatter to consider this."
A failed appeal against the transfer ban last December plunged the Barca board into crisis, playing a part in the firing of sports director Andoni Zubizarreta and Bartomeu's decision to bring forward presidential elections.
"If there wasn't so much tension, then I wouldn't have called the elections," Bartomeu said of the vote taking place at the end of this season.
"I wanted to complete our mandate and the club is functioning reasonably well but I think it was the right thing to do."
Image: Lionel Messi (2nd left) of FC Barcelona celebrates with teammates (left-right) Sandro, Neymar and Sergio Roberto after scoring
Photograph: David Ramos/Getty Images