"I personally, as well as all the members of our board of directors, are firmly convinced that the club has operated well over these years and that the remarks raised against us are not justified," Agnelli said, according to an English version of his speech published by the club.
He added: "Nonetheless, the company will have to continue along the path taken in order to protect the interests of the club and to demonstrate its good and legitimate reasons at each location."
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"For this reason... it is appropriate to take a step back" to avoid a situation where events were influenced by his presence, he said. "Juventus, therefore, comes before everything and everyone."
For a period under Agnelli, Juventus was re-established as one of Europe's best teams.
However, its run of nine straight league titles came to an end in 2021, while its finances have long been in the red.
Shareholders -- led by Exor, controlled by the Agnelli family -- on Tuesday approved revised losses for the 2021/22 season of 239.3 million euros (255 million dollars).
It was the fifth straight set of annual accounts in the red.
Shareholders are set to meet again on January 18 to appoint a new board led by Gianluca Ferrero, a Turin-born former head of coffee brand Lavazza who is trusted by Exor chairman John Elkann -- Andrea Agnelli's cousin.