The Median Tectonic Line (MTL) is the longest arc-parallel fault system in southwest Japan whose right-lateral strike-slip is related to oblique subduction of the Philippine Sea plate (PH). We constructed a dense Global Positioning System network along a 200 km-long traverse line across the MTL in 1998 to estimate deep fault structure and slip distribution. Horizontal velocities were determined at 65 sites through campaign measurements and show crustal shortening in the direction of the plate convergence. Using multi-rectangular segments and depth-dependent coupling at the plate interface, we calculate and remove elastic deformation caused by the PH subduction. The residual velocity field shows right-lateral strike-slip block motion of about 5 mm/yr across the MTL, consistent with geological estimates. However, the block boundary does not coincide with the Surface trace of the MTL, being displaced 20-30 km to the north. The residual velocity field is reproduced by a model with a 35-45degrees northward-dipping fault plane, full locking of the upper portion to a depth of 15 km, and steady slip of 5 mm/yr below. GPS results are supported by imaging of an inclined fault plane revealed by seismic profiling and currently low activity of shallow earthquakes.