The assurance comes amidst Portugal raising objection to the charges invoked by the police against Salem, who was extradited in 2005 for his alleged role in the 1993 Mumbai serial blasts, that entail death penalty.
"I think the judiciary in Portugal has raised some issue. The judiciary here in our country, will take care of them," External Affairs Minister Salman Khurshid said in a joint press conference with his Portuguese counterpart Paulo de Sacadura Cabral Portas.
While getting Salem extradited, India had given an executive assurance to Portugal that it would not slap any charge which would have death penalty and would not keep him behind bars for more than 25 years, key requirements in extradition proceedings in Europe.
Later, Delhi and Mumbai Police slapped charges which entail death penalty against Salem, an accused in several criminal cases, leaving the government and the CBI red-faced.
The Portugal Supreme Court had last year upheld a lower court order cancelling the extradition of Salem for violation of deportation rules by Indian authorities on the grounds that new charges were slapped against him which attracted death penalty.
The Portuguese Foreign Minister said the answers given by India on its questions about Salem are "reasonable".