Karl Prochaska was the son of the Viennese post office official from Moravia of the same name and Marie Prochaska, née Ortner, from Bavaria. In 1917 he left school to serve in the army in Albania. After the First World War he returned as a war invalid to Vienna. In 1918/19 he matriculated as a student of construction engineering for two semesters at the Technische Hochschule in Vienna, but did not sit any examinations. Through the death of his mother in September 1919 – his father had already died in 1911– the tweny-year-old had to break off his studies to look after himself and his younger brother, taking an administrative job in the Kaiser-Franz-Josef-Spital, which was subordinate to the Ministry of Social Administration. After passing the Latin examination in 1921, he also studied modern languages and, from 1923, art history in the Philosophy Faculty of the University of Vienna. In November 1929 he submitted his dissertation on medieval ceiling painting, which was supervised by Josef Strzygowski, at the Institute of Art History. He obtained his doctorate in July 1931, having changed his surname to Ortner the year before. According to his own submission to the Nazi authorities, he had been a member of the NSDAP from 1923 to 1925 but had not been active because his studies took up too much of his time. At the end of 1931 he applied for readmission and in 1932 was given the membership number 898.143. In 1938, Ortner, now a civil servant and art historian, applied to the Ministry of Internal and Cultural Affairs, where he worked in Department II/8 (Human health), for transfer to the Kunsthistorisches Museum (KHM) in Vienna. In November 1938 he started working there as a librarian. Fritz Dworschak, provisional director of the KHM, seconded him in September 1939 to Gaming, where Ortner headed the Bergungsstelle Schloss (Gaming) "in urgent matters of state importance" until 1940, before being succeeded by Karl Pollhammer, so that Ortner was able to return to the KHM library. In 1942 he took leave from the museum to work as a researcher at the Institut für deutsche Volkskunde, Forschungsstelle für Mythenkunde der hohen Schule (Institute of German Ethnology, Higher Education Myth Research Centre) for the NSDAP Reich leadership. He was also a reader on the party examination board and until 1943 head of the Hauptstelle Schrifttum und Büchereiwesen im Schulungsamt des Kreises IV der NSDAP (Literature and Library Main Office of the Education Department in NSDAP district IV). In this function, he claimed after 1945, he transported the collection of Sándor Wolf and the library of his doctoral supervisor Strzygowski to the Reich to save it from being stolen. He was called up to the Wehrmacht in November 1943 and was stationed in 1944 as Oberfeldwebel (staff sergeant) in the Oberfähnrichslehrgang (officer training school) in Bruck an der Leitha. In April 1945 he was taken prisoner in Upper Austria by the US forces.

As a Nazi, Ortner was suspended from the Kunsthistorisches Museum in June 1945. He was classified initially as a minor offender and his suspension from public service was thus reversed in February 1947 under the National Socialist Act. In 1948 the police department in Vienna applied for resumption of the registration proceedings because of Ortner's position as head of the Literature and Library Main Office. He was entered subsequently in the list in 1949 as incriminated and permanently retired in January 1950. His application for reinstatement as curator following the 1957 amnesty was rejected by the Ministry of Social Administration, as was his claim for payment of lost remuneration.