"They were brought to Mumbai and are likely to be produced in the court later," a Central Bureau of Investigation (CBI) spokesperson said.
Salem, a key associate of Dawood Ibrahim, is alleged to have planned and financed the terror blasts in Mumbai that killed nearly 260 people.
He and Bedi were arrested in Lisbon following an Interpol red corner notice issued at the behest of the CBI on Sep 18, 2002.
The extradition follows a prolonged legal battle in various courts of Portugal for over three years.
Salem was sentenced to four-and-a-half years of prison by a Portuguese court after being arrested for carrying a fake passport.
India's request for his extradition had been pending all the while as the country did not have an extradition treaty with Portugal.
India also had to promise Portugal that it would not give capital punishment to Salem.