 Returning to New Zealand, Cotton joined the Department of External Affairs in 1954 and worked in the Specialised Agencies Division of the Department of External Affairs.In a paper to Cabinet in December 1955, he proposed the formation of a cabinet committee to investigate the peaceful uses of nuclear energy in New Zealand.Following Cotton's recommendation, Cabinet established a committee on atomic energy, which studied the reports from delegates to the "Atoms for Peace" conference in Geneva in 1955, and another committee consisting of the permanent heads of government departments with an interest in developing peaceful uses for atomic energy.