After eight productive years at Oxford, Halban was invited back to France in 1954 by the Prime Minister, Pierre Mendès-France, to direct the building of a nuclear research laboratory at Saclay, outside Paris, which greatly expanded the French Commissariat à l'énergie atomique (Atomic Energy Commission).
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The CEA Saclay laboratory developed the independent French nuclear bomb and oversaw the development of French civil nuclear energy.
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In 1942, along with British and other European "refugee scientists", Halban was sent to Montreal as head of the research laboratories at the Montreal Laboratory, part of the nascent Manhattan Project.
In 1944, he took charge of the Canadian Atomic Energy project and became Director of the Montreal Laboratory and Chalk River Laboratories, replacing Hans von Halban, who was considered a security risk.
The Director of the laboratory was Hans von Halban, but he proved to be an unfortunate choice as he was a poor administrator, and did not work well with the National Research Council of Canada.
One of the major strains of the Agreement came up in 1944, when it was revealed to the United States that the United Kingdom had earlier made a secret agreement with Hans von Halban to share nuclear information with France after the war in exchange for free use of a number of patents related to nuclear reactors and filed by Frédéric Joliot-Curie and his Collège de France team.
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He later joined the Anglo-Canadian nuclear program (group of Montreal) in Canada where he joined other Frenchman such as Hans von Halban, Jules Gueron, Pierre Auger, and Lew Kowarski who would join the project in 1944.