The physical origin of Fermi level pinning (FLP) at metal/Ge interfaces has been argued over a long period. Using the Fe$_{3}$Si/Ge(111) heterostructure developed originally, we can explore electrical transport properties through atomically matched metal/Ge junctions. Unlike the conventional metal/$p$-Ge junctions reported so far, we clearly observe rectifying current-voltage characteristics with a measurable Schottky barrier height, depending on the contact area of the Fe$_{3}$Si/Ge(111) junction. These results indicate that one should distinguish between intrinsic and extrinsic mechanisms for discussing the formation of the Schottky barrier at metal/Ge interfaces. This study will be developed for understanding FLP for almost all the metal/semiconductor interfaces.