Following the death of Johan Christian Lund, in 1931, Prior became chief of the General Staff.

[2] Before the Occupation of Denmark by Germany in 1940, Prior encouraged the Danish government to increase the strength of the army.

These requests, however, were not accepted by the majority of the Danish parliament, who feared that increased military strength might provoke Nazi Germany.

The government was also well aware that Denmark's position was untenable; it was too small and too flat to hold out against the Wehrmacht for a sustained period.

Prior continued as Commander-in-Chief of the Danish Army during the early part of the German occupation, and worked actively to prevent the Danish army from becoming involved on the German side during World War II.