Club officials Rinaldo Ghelfi and Marca Branca, as well as the player's agent Carlo Pallavicino, have also been charged individually.
Pallavicino is accused of having brokered a deal with Inter without Lazio's consent.
The club faces the charge of overall responsibility while Ghelfi and Branca are accused of knowingly dealing with Pallavicino behind Lazio's back.
An investigation was opened at the request of Lazio president Claudio Lotito who presented documents to the country's national disciplinary commission relating to the transfer.
Pandev had handed in a transfer request before the start of last season which Lazio refused.
The Macedonia forward was then frozen out of the first team picture for six months before being sold to Inter in January 2010.
He went on to win the treble with his new club in his first half season with the nerazzurri.