German Command was part of the Nazi chain of command in 1936.
By that time, German Command had codenamed a secret submarine pen, supply center and reconnaissance base Geheimhaven, located on an unnamed island north of Crete.
Behind the scenes[]
It's unclear what (if any) branch of the Nazi armed forces "German Command" refers to in Raiders of the Lost Ark Sourcebook as Geheimhaven accommodates both naval submarines and Wehrmacht supplies under the supervision of Wehrmacht captain Mohler. The previous section of the book covering the Wurrfler (U26) refers to the U-boat as taking its orders from "German Supreme Naval Command."