Agnelli's comments were the latest indication that Europe's powerful clubs are unhappy at way the sport is run and turned up the heat on soccer's scandal-plagued governing body FIFA.
"We see our best talents taken away by the national teams for 60 days a year," Agnelli said in Milan in comments widely reported by Italian media.
"Try to imagine the same thing in a private business where the best managers are loaned out for a 'public venture' like a World Cup or European Championship.
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"FIFA is the holder of the rules of the game of football but they are also far away from the interests of the clubs."
Agnelli sits on the executive board of the European Club Association (ECA), which represents more than 200 clubs including top sides like Real Madrid, Barcelona and Bayern Munich.
Juventus are Italy’s most successful club in domestic terms with 31 Serie A titles.
FIFA and ECA could not immediately be reached for comment.
In December, ECA angrily criticised a package of proposed reforms aimed at cleaning up FIFA, which is in the throes of an unprecedented crisis with criminal investigations into the sport under way in the United States and Switzerland.
FIFA’s president Sepp Blatter and European soccer boss Michel Platini have each been banned for eight years. FIFA will choose a president on Feb. 26 at an election where the votes are held by its 209 member associations.
ECA, which will hold its next meeting in Paris on Feb. 8-9, was not involved directly in the reform process and said its members were "not prepared to be further ignored" and were leaving "all options open."
Nearly all the world's top players are with European teams.
FIFA's international competitions depend on a calendar, agreed between FIFA and the clubs, which allow them to be released for their national teams on certain dates.
If the clubs were to pull out of those agreements, it could throw international football into chaos.
Under the calendar for 2016, the players will be available for their respective national teams for 10-day periods in March, September, October and November.
They will also be away for nearly six weeks between May 30 and July 10, when Euro 2016 takes place in France and the Copa America Centenario in the United States.
ECA president Karl-Heinz Rummenigge suggested this month that a European league was a possibility in the future, involving "the biggest teams from Italy, Germany, England, Spain and France."
(Writing by Brian Homewood in Berne, editing by Ed Osmond)
