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Schäfer was born in Hultschin (Hlučín) (today Czech Republic) in the Province of Silesia. He served in World War I in a Field Artillery Regiment. After the war, he participated in far-right Freikorps groups such as the Marinebrigade Ehrhardt and from 1925–28, the Stahlhelm. With Catholic origins, he became a Protestant in 1928, finally designating himself to be a Gottgläubiger, a term employed to describe someone who still believes in God though without any religious affiliation. Like the Communist Party in the USSR, the Nazis were not favorable toward religious institutions, but, unlike the Communists, they did not promote or require atheism on the part of their membership, as early as 1936.
Schäfer joined the Sturmabteilung (SA) in 1933 and was appointed group leader on April 20, 1933. He was an active member of the Sicherheitsdienst (SD), the SS security service, in 1933, and entered the Schutzstaffel (SS) in September 1936. Schäfer took part in the discussion in Berlin on September 21, 1939, with Heydrich, his department chiefs of the RSHA (Reich Main Security Office), and Adolf Eichmann.
During World War II, Schäfer was head of the Nazi security police in Serbia. Between January and May 1942, Schäfer supervised the gassing of around 7,300 Jews in the Semlin camp across the Sava river from Belgrade. A Saurer gas van was used to kill the Jews. In May, Schäfer boasted that "Belgrade was the only great city in Europe that was free of Jews." In Germany after the war, Schäfer was sentenced to six and a half years in prison for his war crimes. Emanuel Schäfer died in 1974 at age 74.