Leaders of the European Club Association demanded a greater voice in decision-making from the governing body.
"I wouldn't say we are at war because the clubs are very patient, but we have a limit," Barcelona president Sandro Rosell said after a meeting of the 197-member group. "What we are asking is rational, logical and fair."
The clubs criticized FIFA for managing the game without proper consultation. The cited confusion over a possible winter switch for the 2022 World Cup in Qatar.
On Monday, FIFA president Sepp Blatter reversed his previous public pronouncements and said it was "settled" to play the tournament in its traditional summer period.
Manchester United chief executive David Gill, an ECA board member, said Europe's clubs and leagues agreed the debate "hasn't been dealt with correctly."
The Qatar debate unsettled the ECA, founded three years ago to give clubs stronger ties with FIFA and the Union of European Football Associations.
"If there are going to be serious discussions in the future then nothing can happen without European clubs," said AC Milan director Umberto Gandini, the ECA vice chairman. "The heart of the game is the European game."
Gandini said FIFA also upset clubs with its management of the international calendar. Clubs think players are left tired and injured because FIFA loads the schedule with too many national team matches - and added eight dates from 2011-14 without telling them.
"All of a sudden, within the powers of the executive committee of FIFA, there is the possibility to modify the international calendar any time of the year," Gandini said.
Gandini insisted Wednesday's slot for international exhibitions was not popular with coaches of national or club teams.
"It's just a nonsense," he said.
Clubs will propose limiting players to one major tournament each year. The 2012 London Olympics kick off less than one month after the July 1 final of the European Championship.
"A players who is in the Euro squad shouldn't be in the Olympic squad," Gill said. "I think common sense will prevail."