Jäger was born in Schaffhausen, Switzerland, and moved with his father to Germany when he was 3 years of age. Jäger enlisted in the German Imperial Army at the start of World War I, where he received the Iron Cross and other awards. After the war, Jäger, an orchestrion maker by profession, obtained a managerial position with the Weber orchestrion factory in Waldkirch. He joined the Nazi Party in 1923 and founded the local party chapter, as a result of which he became known as "Waldkirch's Hitler" among the Alte Kämpfer, as those who had joined before the Reichstag election of September 1930 called themselves. The Weber company went bankrupt in 1931, and he was unemployed for several years. According to his own account, he spurned unemployment benefits from the government of the Weimar Republic, which he despised, so by 1934 he had used up all his savings and his wife Emma separated from him, though their divorce was not formalized until 1940. In July 1933, deputy NSDAP Führer Rudolf Hess had officially decreed that well paid employment was to be found for Alte Kämpfer on a preferential basis. Jäger joined the SS in 1932, and soon had built a 100-strong troop in his small hometown of Waldkirch. His rise within the SS began in 1935, when he was assigned to Ludwigsburg and then to Ravensburg. After attracting the attention of Heinrich Himmler he was called to the Sicherheitsdienst headquarters in Berlin in 1938 where he successfully completed a course of studies, and was promoted to head of the local SD office in Münster in 1939. During the invasion of the Netherlands on 10 May 1940, Jäger was named commander of Einsatzkommando 3, a unit of Einsatzgruppe A. Additionally, Jäger was promoted to the rank of Standartenführer, the equivalent of a colonel in the German army, the same year.
Jäger was instrumental in the brutal and systematic destruction of the Jewish community of Lithuania. From July 1941 until September 1943 Jäger served as commander of the SD Einsatzkommando 3a, a sub-unit of Einsatzgruppe A under Franz Walter Stahlecker, in Kaunas. Under Jäger's command, the Einsatzkommando, with the help of Lithuanians, shot Jewish men, women and children indiscriminately. It perpetrated the Ninth Fort massacres of November 1941. During this time, reports detailing calculated acts of mass murder were routinely submitted to his superiors. Some of these reports survived the war and are collectively referred to as the "Jäger Report" from 2 July 1941 to 25 November 1941 . Reassigned back to Germany near the end of 1943 after a nervous breakdown occasioned by the mass murders he had participated in, Jäger was appointed commander of the SD in Reichenberg in the Sudetenland, and precluded from further promotions due to what the SS saw as a "lack of strength of nerve."
The actions by Einsatzkommando 3, including the Rollkommando Hamannkilling squad were tallied by Jäger himself. The report keeps an almost daily running total of the liquidations of 137,346 people. The "Jäger Report" provides a detailed account of the murderous rampage of this "special squad" in Nazi-occupied Lithuania.
Escape, capture, and suicide
Jäger was able to assimilate back into society as a farm hand until his report was discovered in March 1959. Arrested and charged with his crimes, Jäger committed suicide by hanging himself in prison in Hohenasperg while he was awaiting trial in June 1959.