The 34-year-old BMC Racing rider is implicated in the scandal and the IOC has charged him with a violation of article 2.2 of the World Anti-Doping Agency Code, namely "use or attempted use by an athlete of a prohibited substance or a prohibited method".
Ballan was briefly withdrawn from competition by his BMC Racing team in 2010 as the inquiry began.
Press Association Sport has contacted Ballan's BMC Racing team and is awaiting a response.
A statement on coni.it read: "Athlete Alessandro Ballan has been referred to the Second Chamber of the National Court of CONI Anti-Doping for the recognition of responsibility for the violation of article 2.2 of the WADA Code, on the basis of the documents submitted by the public prosecutor of Mantova, with requests for two-year suspension."
The anti-doping prosecutor of CONI also recommended a lifetime ban for pharmacist Guido Nigrelli and a seven-year suspension for doctor Fiorenzo Egeo Bonazzi, who are accused of trafficking and administering prohibited substances.