After the 1971 war with India, the government sent Ishfaq Ahmad to the Pakistan Institute of Nuclear Science and Technology (PINSTECH). When Munir Ahmad Khan became the chairman of PAEC and was put in charge of secret atomic bomb project, Munir Khan appointed Ahmad as the director of PINSTECH, where he remained up to 1976. Ahmad served as the director of the Nuclear Physics Division at the secret Pinstech Institute which developed the first designs of atomic bombs, a clandestine project during the post-1971 war. There, he played an influential role in leading the physics and mathematical calculations in the critical mass of the weapons, and did preliminary theoretical work on the implosion method used in the weapons.