The leadership of the AIA learned about the arrest of D'Onofrio as part of an investigation into international drug trafficking with utter dismay.
The operation resulted in 42 arrests two days ago in the Milan area.
D'Onofrio, a former soldier, has resigned from his post as chief prosecutor for the AIA according to ANSA.
AIA President Alfredo Trentalange reportedly announced the resignation without going into any details for the reasons.
According to the investigations conducted by the DDA from 2019 to 2021, the 42 arrestees of various nationalities allegedly imported six tonnes of marijuana and hashish into Lombardy.
Almost half a ton of drugs plus a thousand cannabinoid-based electronic cigarette refills were seized during the operation, La Gazzetta Dello Sport reported.
D'Onofrio joined the AIA in 2013 and was later appointed chief prosecutor under president Trentalange. The office is responsible for investigating possible irregularities in refereeing in Italy.