IOC president Jacques Rogge and FIFA head Sepp Blatter have written a joint letter to the European Commission protesting about proposed changes to the way sport will be run in the European Union (EU).
A source close to the matter has told Reutersthat the letter was also sent to each of the Union's 25 sports ministers.
"To say the letter is strongly worded is putting it mildly," the source said. "It basically is telling the commission and the ministers to mind their own business."
A European Sports Review completed in April recommends closer control of sport in the EU including salary caps on soccer players and the monitoring of agents.
The chief executive officer of the European governing soccer body UEFA Lars-Christer Olsson said many of the game's problems had been created by legal uncertainty.
We are simply seeking legal clarification to tie up these loose ends," he said.
"Sport is different to other businesses but we are not above the law.
"We just want to work in a partnership with the EU authorities to help solve these problems."
A UEFA source said FIFA had to realise the EU needed European solutions for European problems.
"To be honest most of the problems that we currently have in the game are of FIFA's own making," the source said.