Despite a number of achievements in his 19 years in the job, he will be remembered in Pakistan chiefly for being removed as head of the Bomb project in 1976, and also for his long and bitter rivalry with A.Q. Khan, his de facto replacement, who is widely credited with achieving what Munir Khan failed to do.
Munir was one of Pakistan's most enigmatic figures. To the many who knew him well, he was a patriot, a voice of reason who was committed to international safeguards for Pakistan's nuclear technology, and who would despair whenever politicians reached for the nuclear card. But others in Pakistan's nuclear establishment believe that he was against Pakistan acquiring bomb-making technology.
Munir's other crime in their eyes was his strong ties to the West - where he lived and worked for nearly two decades. In Pakistan's increasingly isolationalist political climate, public figures with overseas links are often discredited by opponents as a threat to national security.
Munir's 40-year association with the International Atomic Energy Agency (IAEA) in Vienna - as a member of its scientific staff, and later its board of governors, which he also chaired - was seen by his enemies as evidence of his questionable loyalty to the country of his birth.
In truth, Munir and AQ represent two strands of thinking in Pakistan's defence and foreign policy. Munir represented a dying generation who live in the hope that Pakistan will one day play an influential role in world affairs by maintaining friendships and alliances with the West. AQ, on the other hand, represents a growing constituency, which believes that the security interests of Western countries are incompatible with those of the Muslim world.
Munir Ahmad Khan was born in 1926 in British India - now Pakistan. He was educated at Government College, Lahore, and left for the United States on a Fulbright Scholarship in 1951. After completing a masters degree in electrical engineering, he joined the Argonne National Laboratory in Illinois where he trained as a reactor engineer. In 1958, he joined the IAEA, where he served in the division of nuclear power and reactors until 20 January 1972, when Zulfikar Ali Bhutto, Pakistan's newly elected prime minister, propelled him to the top of Pakistan's Atomic Energy Commission.
Bhutto had met Munir several times before. Munir's brother, Khurshid, was a law minister in the government of Field Marshal Ayub Khan when Bhutto was Minister for Natural Resources. He occasionally sought Munir's advice on nuclear matters on visits to Vienna. But the meeting on 20 January 1972 was to be different.
Bhutto had just taken over as prime minister under controversial circumstances of a dismembered country that had lost a war to India, and half its population to independent Bangladesh. India, moreover, was suspected of having atomic ambitions.
Bhutto summoned the country's leading scientists to a meeting at Multan, 150 miles south-west of Lahore. Among the issues discussed was whether Pakistan could build the Bomb. The audience included Pakistan's chief scientific adviser, Abdus Salam, who would later win the Nobel physics prize. Another key figure was I.H. Usmani, the then chairman of the atomic energy commission who had carefully and painstakingly built up Pakistan's nuclear power infrastructure over the previous decade.
Both are understood to have tried to dissuade their new prime minister from devoting resources to developing an atomic bomb. But Bhutto's mind was apparently made up, and he announced that Munir would replace Usmani, who was moved to head the newly created Ministry of Science and Technology.
Pakistan's efforts to go nuclear accelerated after the first Indian nuclear tests in May 1974. Initially, it followed the plutonium route to building a nuclear device. (Plutonium is one of the by-products of fuel that has been reprocessed from nuclear power plants.) And in October 1974, Pakistan signed a contract with France for the design of a reprocessing facility for the fuel from its power plant at Karachi and other planned facilities.
By that time, however, all of Pakistan's overseas nuclear collaborators were pulling out as rumours of Pakistan's nuclear ambitions spread. The French were among the last to pull the plug following sustained pressure from the United States.
Pakistan at this stage had little choice but to pursue highly enriched uranium as a route to its nuclear device. And in 1976, it aquired the services of A.Q. Khan, a metallurgist from the Netherlands, who was also an expert in uranium enrichment. AQ worked under Munir for a short period. But the pair fell out, and in July 1976, Bhutto gave AQ autonomous control of the uranium enrichment project reporting directly to the prime minister's office - an arrangement which exists to this day.
Munir continued to serve as head of the PAEC and concentrated on, among other things, strengthening the education and training of nuclear scientists and engineers. After retiring in 1991, he maintained an active interest in science policy, and went on to chair a technology foresight exercise.
His precise role in Pakistan's failed efforts to acquire a plutonium bomb will probably never be known. The Indian test of 1974 and France's decision to cancel Pakistan's reprocessing facility is a key reason for failure. But Munir's own reluctance to circumvent international nuclear safeguards is undoubtedly another.
To construct a plutonium bomb, Munir would have had to authorise the illegal diversion of fuel from the Karachi nuclear power plant (Kanupp). As a a committed member of the IAEA, and a strong supporter of the concept of a global nuclear safeguards regime, Munir Khan would have been uncomfortable with this idea. But France's decision not to go ahead with the planned reprocessing plant saved him from what would have been a difficult test of his loyalty.
Munir Ahmad Khan, nuclear power engineer and civil servant: born Islamabad, India 20 May 1926; married (three children); died Vienna 22 April 1999.