Singh was reacting to a US court awarding a 35-year-jail term to the Lashkar-e-Toiba operative who scouted for possible targets ahead of the 26/11 Mumbai attacks.
The home secretary also reiterated New Delhi's position - echoed earlier by external affairs minister Salman Khurshid - that Headley should be extradited.
Headley had negotiated a bar on death penalty and his extradition right at the beginning of legal proceedings in his plea bargain agreement.
The UPA government had initially pointed to these provisions to indicate his extradition might be difficult but hardened its public position after the opposition BJP accused the home ministry of going soft.
Singh's statement on Friday was a continuation of this posturing.
He said New Delhi would continue to press for Headley's extradition despite terms of his plea bargain.