State prosecutors had originally charged Shamir with "grave espionage," but following talks between the prosecution and defense in the case in recent weeks, it was decided to charge him with the lesser charge of "contact with a foreign agent" and possessing information with the intent of using it to harm the State.
Shamir, 45, was arrested by the Shin Bet in cooperation with the police's Severe and International Crimes Unit. He is expected to plead guilty to the revised charges.
There is currently no agreement on what kind of punishment he will receive.
During court discussions on the Shamir case, state prosecutors argued that the doctor had been exposed to classified material as a result of his service as an IDF mental health officer in the reserves.
They argued that he had had access to IDF Medical Corps emergency plans including the methods of medical corps deployment, the way in which services are administered to the Home Front Command during times of war, citizen evacuation plans in the case of missile attacks and various other intelligence formations.
In the original charge sheet, Shamir was accused of "making contact via e-mail with the Iranian Foreign Ministry.
He presented himself in the e-mail as an Israeli officer well-informed with goings-on in Israel and noted that he was a well-connected member of Israeli society."