A report by news agency Belga says that Lefevere left the decision to race in Boonen's hands but the former points classification winner is doubtful over whether he will ever return to the Grand Boucle.
"The chances of that happening are very low," he said with six Tours de France under his belt and six stage wins. "Maybe I will never return."
It's been a frustrating 2013 for Boonen who crashed out of the Tour of Flanders after hitting a road sign. His off-season was punctuated by intestinal problems and then a severely infected elbow.
"I do not want to force it," said Lefevere. "A rider who fears the event that lasts three weeks, [I] do not force him to change his mind.
"I confess I would have preferred to see him at the start in Corsica. For advertising it would have been a serious bonus. It will be otherwise."
Instead of the Tour de France, Boonen will instead race the Tour de Wallonie (July 20-24) and the Tour of Poland (July 27 - August 3).
When Omega Pharma - Quick-Step unveiled their 2013 roster at the Gent velodrome in January, Boonen raised the possibility of a return to the Tour de France, having not raced since 2011, and playing a role in the lead-out for Mark Cavendish. Those thoughts now have been put by the wayside for now, perhaps in the wake of the Manx Missile's success at the Giro d'Italia with four stage wins to his name so far.
"Would I have been the perfect teammate Mark Cavendish? I think it would be crazy to put me in his lead-out," suggested Boonen. "His men must continue to work together."