Scaroni and the company is the subject of an investigation in Milan. Eni is under investigation for what The New York Times described as "suspicious payments" of around $268 million related to contracts for its oil subsidiary Saipem in Algeria.
"Eni and its CEO declare themselves totally unrelated to the object of investigation," the company said in a statement.
Eni acknowledged it was the target of the Milan investigation but suggested it took corrective action when corruption allegations surfaced in November.
"Eni has also directly provided, and will continue to provide, full cooperation with the prosecutor's office," the company said.
No charges have been filed in the Milan case.
Eni in April said it received a "judicial request" from the U.S. Securities and Exchange Commission for documents related to its work in Libya from 2008-11. The subpoena was related to alleged payments made to Libyan officials in violation of the U.S. Foreign Corruption Practice Act.
Eni, one of the first energy companies to return to Libya last year, generated 13 percent of its revenue from operations there before the war.