Jean-Michel Aulas is "pessimistic" over the sale of the 28-year-old, who could now be forced to stay at Stade Gerland rather than make a move before the end of the transfer window
The France international was believed to be edging towards a move to the Premier League outfit this summer after the clubs agreed a 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.