The CBI had earlier told the Supreme Court that it wanted to withdraw certain charges under TADA Act, Explosives Substances Act, Arms Act and Explosives Act in view of its commitment to the Portugal government.
Special CBI Prosecutor Deepak Salvi on Tuesday filed an application in the court saying they want to drop certain sections from the 1993 bomb blasts case.
On August 5, the apex court had said the extradition of 45-year-old Salem to India is still valid, despite its termination by the Portugal's Constitutional Court.
At the time of Salem's extradition, India had assured Portugal that no charges entailing death penalty or imprisonment of more than 25 years would be pressed against him but such charges were later brought in.
Special Judge G A Sanap allowed the CBI to withdraw charges. Salem, an accused in the 1993 Mumbai serial blasts, was extradited from Portugal on November 11, 2005, after a prolonged legal battle.
The Supreme Court of Portugal had last year dismissed an appeal of the CBI, challenging termination of extradition of the underworld don.
Salem was shot at by gangster Devendra Jagtap alias JD, an accused in the murder of advocate Shahid Azmi who had represented an 26/11 Mumbai attack accused, in Taloja Central Jail in Navi Mumbai on June 27. Salem was hit in his hand by one of the two rounds allegedly fired by JD.
Earlier, his lawyers had said that they would move the European Union (EU) seeking execution of the order canceling his extradition to India issued by the Portuguese Constitutional Court.