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.
Kowarski then worked in the Montreal Laboratory in Canada, but only after Halban had been replaced as Director by John Cockcroft, as he did not want to work under Halban.
While he maintained that he did not divulge any nuclear secrets to his previous boss (although he had discussed patent rights), Halban was not allowed to work or to leave North America for a year, by General Groves, head of the Manhattan Project.
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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.
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In January 1943 the Cambridge team including Nunn May transferred to the Montreal Laboratory which was building a reactor at Chalk River near Ottawa, Canada.
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.