Jean-Michel Aulas claims other clubs have tried to scupper the striker's proposed transfer to Newcastle by launching "dishonest" bids
The France international was believed to edging toward a move to the Premier League outfit this summer after both clubs agreed a €10 million fee for the striker.
However, Aulas revealed the deal could still go "haywire" this week as negotiations continued to stutter, and he has now involved the LFP in an attempt to root out those who he claim have tried to scupper the deal.
He told L'Equipe: "I am disappointed because the deal was not finalised with Newcastle and I'm pessimistic over the transfer now.
"I filed a complaint because certain clubs were unsettling certain players. Some offered dishonest proposals to try and derail the deal.
"I will let the committee settle it."
Aulas went on to confirm that the 28-year-old, whose current deal expires next summer, would remain at Stade Gerland if his future is not clarified by the end of the transfer window.
He added: "Gomis will be reintergrated into the squad if he is not transferred."
The Magpies have since secured a deal to sign QPR striker and fellow Frenchman Loic Remy on loan until the end of the season, casting further doubt over a deal for Gomis.