I found this by accident when looking for something else,
Japan's shortest railway tunnel, the Tarusawa tunnel on JR East in Gunma. Total bore length, 7.2 meters (yes, you read that right).
Apparently the line was built during the war, as a rush job, but why they bored through the outcrop rather than removing what little stone remains above it is unclear.
http://www.youtube.com/v/VZCGlQ5_oPcThere's a prototype for everything.