He worked with Bruno Beger on some projects, making measurements of Jewish people. He was with Beger at Auschwitz when the people were selected to be part of the Jewish skeleton collection, a project of the Ahnenerbe. At their post-war trial, Beger was found guilty of full knowledge of the scope of that project, while Fleischhacker was found not to be aware that the purpose of the measurements was to select the 86 people to be murdered at Natzweiler-Struthof camp.