Italian Rossi kicked last year's champion Marquez off his bike at the Malaysian Grand Prix on Sunday.
"The recent events arising in connection with the competition for the 2015 world title have had a damaging effect on the staging of our competitions and poisoned the atmosphere around the sport," Ippolito said in a statement on the FIM website.
"We are moving away from the tradition of pride in sportsmanship that is part of the heritage of motorcycling."
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Rossi finished third in Sunday's race won by Dani Pedrosa but was handed three penalty points.
He will start the last grand prix of the season in Valencia, Spain on Nov. 8 from the back of the grid, seven points ahead of Spain's Jorge Lorenzo in the standings.
Rossi had said Marquez deliberately tried to impede him during this month's Australian Grand Prix to help Lorenzo.
"Everyone has the right to express his or her own ideas. But words and actions always have consequences. Every individual has to take responsibility for those consequences," Ippolito said.
"The riders, first of all, must be aware of this. Their responsibility is also shared by the people who form their entourage.
"Whatever the rights and wrongs of the matter, if some of those people unnecessarily fuel polemics about events or decisions in a wrongheaded way, they are doing a great disservice to the sport, to the detriment of our entire community and all the good things it offers to everyone."
Ippolito hopes to lead a happy conclusion to the world title race.
"I express the hope that at the next and final round in Valencia the riders will fight it out on the track and in a way that fully respects the spirit of fair play," he said.
(Reporting by Ed Osmond; editing by Toby Davis)
