PAEC advocates increased nuclear energy generation to overcome serious energy shortages in a country substantially lacking in natural energy resources. In an effort to accelerate Pakistan's overall economic development, the commission also promotes the utilization of nuclear technologies in other areas, i.e., to enhance agricultural production and for medical diagnosis/therapy.The head of the PAEC, Dr. I. J. Usmani, and Abdus Salam [who won the Nobel Prize in 1979], worked to establish Pakistan's first nuclear power reactor called Kannupp, near Karachi as well as with PINSTECH and SUPARCO. I. H. Usmani, the chairman of the PAEC who had carefully and painstakingly built up Pakistan's nuclear power infrastructure over the previous decade, tried to dissuade Zulfikar Ali Bhutto, Pakistan's newly elected prime minister, from embarking on a nuclear weapons program. Following the fateful Multan conference, Bhutto announced Usmani would head the newly created ministry of science and technology.
Usmani and Abdus Salam resigned in 1974 when Zulfiqar Ali Bhutto wanted to take the development of nuclear technology to, in his words, "its natural conclusion" i.e. the build up of nuclear weapons. Both Usmani and Salam disagreed with this policy.
On 20 January 1972, Bhutto appointed Munir Ahmad Khan head of the PAEC. Munir Ahmad Khan had joined the IAEA in 1958, where he served in the division of nuclear power and reactors until moving to the PAEC. A.Q. Khan initially worked under Munir Ahmad Khan's Pakistan Atomic Energy Commission for a short period. But the pair fell out, and a long and bitter rivalry followed. In July 1976, Bhutto gave A.Q. Khan autonomous control of the uranium enrichment project, reporting directly to the prime minister's office, which arrangement has continued since. Munir, who was criticized in some circles as being against Pakistan acquiring nuclear weapons, remained as head of the PAEC for 19 years until his retirement in 1991 [he died in April 1999].