He joined the NSDAP in 1938. Murer was trained with Hitler Youth in Nuremberg. He was then transferred to Vilnius and was from 1941 to 1943 responsible for Jewish affairs as deputy of Territorial Commissioner (Gebietskommissar) Hans Christian Hingst. He was known as a sadist who showed special cruelty towards the Jews. Vilnius, which was known as "the Jerusalem of Lithuania" before the war, had a Jewish population of about 80,000. After the war around 250 Jews were living there. The rest had been murdered by the SS and Murer was instrumental in organizing these killings. On July 1, 1943 Murer was replaced by Gestapo man Bruno Kittel to liquidate the ghetto.
After the war Murer moved to Steiermark in Austria. Near his residence in Admont there was a camp for displaced persons. In 1947 one of these DPs recognized Murer and British forces arrested Murer. In December 1948 he was deported to the Soviet Union since Vilnius had been under Soviet jurisdiction. He was found guilty of having murdered Soviet citizens and sentenced to 25 years of hard labour. As a part of the Austrian State Treaty, he was released in 1955 and thus returned to Austria. Simon Wiesenthal managed to get him prosecuted again in 1963. The trial that took place in Graz, Austria, lasted for a week and ended with the acquittal of Murer.
- (in Russian) Добрый дедушка Франц из Гайсхорна, или удивительные метаморфозы Франца Мурера
- The Complete Black Book of Russian Jewry, p. 370
- The Complete Black Book of Russian Jewry, p. 249
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