In 1933, Mälzer received a certificate as a graduate engineer (today's equivalent to a Master's degree) and was thereafter assigned to the German Ministry of Defense.

Promoted to Oberst (Colonel) in 1939, upon the outbreak of World War II Mälzer was assigned as a staff officer of Luftflotte 2.

Promoted to Generalmajor in 1941, he became a Department Head in the German Ministry of Aviation until September 1943 when he transferred to command Flugbereitschaft 17 in Vienna.

Since Rome had become a city close to the front, the power to decide about retaliatory measures after partisan attacks lay with the commanders of the Wehrmacht, i.e. Mälzer, Eberhard von Mackensen and Albert Kesselring.

[1]: 51  Shortly after the bombing of the German SS Police Regiment 'Bozen' on 23 March 1944, an apparently intoxicated Mälzer appeared at the scene of the crime and ordered to blow up the blocks of houses at the Via Rasella immediately.

In their respective trials after the war, Mälzer, Mackensen and Kesselring claimed that they acted under direct order from Adolf Hitler, and that the shooting of 330 Italians already sentenced to death was to be planned and carried out by the SD under Kappler.

[1]: 58  On the witness stand Kappler argued that he had received orders from Kesselring,[1]: 137  and suggested that at least Mälzer knew that the Germans did not have 330 prisoners under the sentence of death.