In 1972, Khan officially resigned from his directorship of the IAEA's reactor division when he was appointed as chairman of the
Pakistan Atomic Energy Commission, replacing
I. H. Usmani who was appointed secretary at the
Ministry of Science in the Bhutto administration. On 28 November 1972, Khan, together with Abdus Salam, accompanied President Bhutto to the inauguration ceremony for the
Karachi Nuclear Power Plant (KANUPP)–the first milestone towards the goal of making Pakistan a nuclear power. Khan played a crucial role in keeping grid operations running for the Karachi Nuclear Power Plant after its chief scientist,
Wazed Miah, had his
security clearance revoked, and was forced to migrate to
Bangladesh. Negotiations with France over the reprocessing plant was extremely controversial at home with the United States later intervening in the matter between Pakistan and France over fears of nuclear proliferation.
1971 war and atomic bomb project On 16 December 1971, Pakistan ultimately called for a unilateral ceasefire to end their
third war with India when the
Yahya Khan administration acceded to the
unconditional surrender of the
Pakistani military on the eastern front of the war, resulting in the
secession of East Pakistan as the independent country
Bangladesh, from the Federation of Pakistan. Upon learning the news, Khan returned to Pakistan from
Austria, landing in
Quetta to initially attend the winter session to meet with PAEC's scientists before being flown to
Multan. This winter session, known as the
"Multan meeting", was arranged by Abdus Salam for scientists to meet with President Bhutto who, on 20 January 1972, authorized the
crash program to develop an
atomic bomb for the sake of "national survival". President Bhutto invited Khan to take over the weapons program work—a task that Khan threw himself into with full vigor. In spite of having been unknown to many senior scientists, Although Khan was not a
doctorate holder, In a short time, Khan impressed the conservatively-aligned
Pakistani military with the breadth of his knowledge, and grasp of engineering,
ordnance, metallurgy, chemistry, and interdisciplinary projects that would distinguish from the field of physics. In December 1972, Abdus Salam directed two
theoretical physicists,
Riazuddin and
Masud Ahmad, at the International Center for Theoretical Physics to report to Khan on their return to Pakistan where they formed the "Theoretical Physics Group" (TPG) in PAEC— this division eventually went to commit itself to perform tedious mathematical calculations on fast neutron temperatures. Salam, who saw this program as an opportunity to ensure federal government's interest and funding to promote scientific activities in his country, took over the TPG's directorship with Khan assisting in the
solutions for
fast neutron calculations and binding
energy measurements of the atomic bomb. The research operational scope of the
Pakistan Institute of Nuclear Science and Technology, the national laboratory site, was well expanded from a school building to several buildings, which were erected in great haste, in
Nilore. In March 1974, Khan, together with Salam, held a meeting at the Institute of Nuclear Science and Technology with
Hafeez Qureshi, a mechanical engineer with an expertise in
radiation heat transfer, and Dr. Zaman Shaikh, a chemical engineer from the
Defense Science and Technology Organization (DESTO). At that meeting, the word "
bomb" was never used but it was understood the need for the development of
explosive lenses, a sub-critical sphere of fissile material could be squeezed into a smaller and denser form, and the
reflective tamper, the metal needed to
scatter only very short distances, so the critical mass would be assembled in much less time. Eventually, the project was relocated to the ML with Qureshi and Zaman moving their staff and machine shops from the Institute of Nuclear Science and Technology with assistance from the military.
Nuclear tests: Chagai-II In 1975, AQ Khan, in discussion with the Corps of Engineers, had selected the
mountain ranges in
Balochistan for the isolation needed to maintain security and secrecy. Preparations for the tests and engineering calculations were validated by Khan with Ahmad leading the team of scientists; other invitees to witness the test included
Ghulam Ishaq Khan, Major-General
Michael O'Brian from the
Pakistan Air Force (PAF), General
K. M. Arif,
Chief of Army Staff at that time, and other senior military officers. By 1979, Khan removed PAEC's role in defense production moving the Wah Group, that designed the
tactical nuclear weapons in 1986, from ML to
KRL, and also founded the
National Defence Complex (NDC) in 1991. While attending a conference on nuclear safety in Austria, Khan became acquainted with Indian physicist
Raja Ramanna when discussing topics in nuclear physics, briefly inviting the latter for a dinner at the
Imperial Hotel where Ramanna confirmed the veracity of the information. In 1990, Khan advised the
Benazir's administration to entered in negotiation with France over construction of nuclear power plant in Chashma. As chairing the PAEC in 1972, Khan played a crucial role in expanding the "
Reactor School" which was housed in a lecture room located at the Institute of Nuclear Science and Technology in Nilore and had only one faculty member, Dr. Inam-ur-Rehman, who often traveled to the United States to teach engineering at the
Mississippi State University. In 1976, Khan moved the
Reactor School in Islamabad, renaming it as "
Centre for Nuclear Studies (CNS)" and took the professorship in physics, as an unpaid
part-time employment, alongside Dr. Inam-ur-Rehman. After his retirement from PAEC in 1991, Khan went to academia when he joined the faculty at the center for nuclear studies as a full-time professor to teach courses on physics while continuing to push for the CNS to be granted as university by the
Higher Education Commission. In 1997, his dream was fulfilled when the federal government accepted his recommendation by granting the status of center for nuclear studies as a
public university and renaming it as the
Institute of Engineering and Applied Sciences (PIEAS). ==Final years==