Scaroni told CNBC he was shocked by the decision, which he said referred back to events that took place between 2002 and 2005.
"I am in no way involved in this matter and will appeal immediately," he told CNBC in an statement emailed by an Eni spokesperson.
"I am surprised by this decision – as the defense has shown, the Enel Porto Tolle plant has always operated within legal standards," Scaroni added.
The Italian court said in the document seen by Reuters that the CEO of utility Enel, Fulvio Conti, had been acquitted in the case.
Scaroni's lawyer, Alberto Moro Visconti, confirmed his decision to appeal.
"The charges have no grounds. In addition, they date so far back that, had they occurred, they would have already been time-barred. The decision is inexplicable," he told CNBC in a statement emailed by Eni.