Lomanitz's graduate research was cut short when the Counterintelligence Corps ensured he was drafted into the Army during World War II.
While at the Radiation Laboratory, Lomanitz helped to establish a local chapter of the Federation of Architects, Engineers, Chemists, and Technicians (FAECT), a small white-collar communist-aligned CIO union.
[3] The Federal Bureau of Investigation had placed a listening device in the residence of Communist Party activist Steve Nelson, and in October 1942 overheard a man referred to as "Joe", whom the FBI suspected of being Lomanitz's close friend Joseph Weinberg, describing to Nelson the significance and technical outlines of the secret nuclear research done at Berkeley.
He adamantly asserted his loyalty to the United States and invoked the Fifth Amendment, and declined to name others involved with Communist activities.
The Atomic Energy Commission Personnel Security Board (PSB) found in 1954 that Oppenheimer had stated in 1943 that he did not want anybody working on the project who was a member of the Communist Party, since "one always had a question of divided loyalty" and the discipline of the Communist Party was very severe and not compatible with complete loyalty to the project.