Ernst Egger was born in Vienna as the son of the industrialist Bernhard (Bela) Egger (1831–1910). He worked for some time in the USA as a building engineer and later became president of Vereinigte Glühlampen und Elektrizitäts-Aktiengesellschaft (Tungsram) in Ujpest, Hungary, a company founded by his father. Egger was also vice-president of N.Ö. Eskomptegesellschaft and from 1934 member of the board of its successor company Österreichische Industriekredit AG, Am Hof 2, in Vienna's 1st district. Within the Bund der österreichischen Industriellen (Federation of Austrian Industrialists), he chaired the Verband der Gaswerke (Gasworks Association) and was a member of the board of the Fachverband der Elektrizitäts-, Gas- und Wasserwerke (Professional Association of Electricity, Gas and Waterworks). His brother Adolf Egger (1874–1964) founded Fiat Werke Aktiengesellschaft in Vienna in 1907. From 1933 until at least 1936, Egger was a member of the management of the Verein zur Förderung des Technischen Museums Wien (Association for Promotion of the Technisches Museum Wien). His name was deleted from the membership list in 1938 with the comment "Jew". The Österreichisches Forschungsinstitut für Geschichte der Technik (Austrian Research Institute for the History of Technology) in the Technisches Museum was commissioned and paid by Ernst Egger to write a biography of his father. After the annexation, the Institute ceased this work on account of Bela Egger's Jewish origins. The Institute director, Ludwig Erhard, advised Egger to publish "this life story as a family chronicle" himself. Although baptized a Protestant, Egger was persecuted by the Nazi regime as a Jew under the Nuremberg Laws. He was registered until May 1944 in his apartment at Mommsengasse 25 in Vienna's 4th district. On 28 June 1944 he was deported to Theresienstadt, where he perished on 9 December 1944. His wife was arrested and died in June 1944 in the prison at Rossauerlände 7–9. The two daughters were also deported. While Elisabeth Ilka Egger was murdered in Auschwitz, her sister Marianne survived Theresienstadt.

Ernst Egger had already donated objects to the Technisches Museum Wien before 1938 and continued to do so after the annexation. In autumn 1938, for example, he gave the museum an Edison tube, four glass plate negatives and a benchtop scale, the only one of these items to be found in the depot in the Museum's general inventory. In 2006 the Art Restitution Advisory Board recommended the restitution of the letter balance to the heirs.