The coach of last season's Serie A champion has been accused by the FIGC of failing to report unsporting behaviour while at his former club Siena.
Pepe is deferred for the same reason as Conte, who could face a six-month ban if found guilty, while Bonucci faces allegations of actively influencing a result during his days as a Bari player.
None of the trio are under suspicion of illicit behaviour since arriving at Juventus, which is extraneous to the current investigation which could have far-reaching effects in Italian football, especially in the lower leagues.
A statement from FIGC read: "Thirteen clubs and 45 individuals have been deferred to the disciplinary committee as part of the investigation into betting in football, related to the investigation by the Cremona and Bari public prosecutors office.
"The Federal (FIGC) prosecutors have deferred Lecce and Grosseto for direct responsibility while Ancona, Siena, Novara, Torino, Varese, Albinoleffe, Bari, Udinese, Portogruaro, Sampdoria and Bologna have been deferred for strict liability.
Serie B clubs Lecce and Grosseto both face the prospect of relegation to the third division while Serie A side Siena could be docked points.
Games involving those clubs, and many others, have been examined by the FIGC as part of an investigation into match-fixing, leading to these deferrals.
The first hearings are set to take place next week in order to determine sanctions before the start of the 2012-2013 season.
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