Earlier on Friday, the Bianconeri chief publicly criticised the governing body for Italian football as coach Antonio Conte will go on trial to prove his innocence in the Scommessopoli scandal after his plea bargain deal was rejected by magistrates.
Agnelli had accused the FIGC of operating on a 'dictatorial system', and the federation has now come out to criticise the comments made by the Juventus supremo.
"The FIGC and its administrative bodies operate in the full respect of the rules which guarantee the independence and autonomy of the sporting justice," a FIGC statement read.
"The comments made by Juventus president Andrea Agnelli are unacceptable and go beyond the legitimate right to criticism.
"They also contrast with the statements he made on July 26, in which the natural sadness at the charges was - in his own words - 'mitigated by the knowledge that the rules of the sporting justice system will achieve clarity in this match which is played in front of the various courts.'"
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