In 1940, when Germany invaded Norway as part of World War II and the royal family and government of Norway fled the country, Schei was specifically asked to stay in Norway, where he continued as director of provisioning and rationing until 1945. As a civil servant Schei was one of the many people who worked throughout the war without being favoured by the new Nazi authorities. In addition, Schei was involved in the Norwegian resistance movement, as a clandestine member of Hjemmefrontens Ledelse. He was imprisoned briefly in Akershus Fortress in 1944, and also survived an assassination attempt. Similarly, Carl Platou also continued in his position, but was eventually imprisoned for secret resistance work. His father-in-law Ingolf Elster Christensen came to be the leader of the Administrative Council, which was abolished in September 1940.