Gillingham midfielder Luke Rooney was left out of Andy Hessenthaler's squad for Saturday's 2-1 win at Aldershot after rejecting a new contract.
Talks with the 20-year-old Gills youth product have reached stalemate, forcing Hessenthaler's hand.
"We've offered a new deal and come to loggerheads," said Hessenthaler. "We'd love him to sign but we don't think he's going to sign the improved offer.
"There's nobody bigger than the football club," he told BBC Radio Kent.
"I only want players who are committed to getting us out of this division so, at the moment, he won't be in the squad."
Fellow midfielder Jack Payne this week signed a new contract keeping him at the club until the summer of 2015.
But Hessenthaler now appears resigned to losing Rooney -who has scored nine times in 33 league starts for the club - next summer.
"We had one that signed a two-year extension," said Hessenthaler. "These are the players we want to work with.
"But, although we made Luke a very good offer, they're adamant they're not going to sign it.
Speaking after a victory at Aldershot that lifted his side to eighth in League Two, Hessenthaler added: "Whatever happens, if he leaves in the summer, there's compensation because he's under the age of 24.
"He's proved to me he's a very good player but, if the boot was on the other foot, and he was the manager or chairman, he'd want players who are committed to the club."