For many years, the generation mechanism of disastrous intraplate earthquakes in the upper plate of a subduction zone have remained unclear largely because the roots of upper plate intraplate faults have particularly quiet inter-seismic nature and limited visibility. Here we propose that the 2008 Mw 6.9 Iwate-Miyagi Nairiku, Japan, Earthquake, occurred on a dipping fault in a volcanic region, contains previously-unreported co-seismic evidence of a ductile shear zone (DSZ) present on the down-dip fault extension beneath the seismogenic layer, and DSZ plays a dominant role in the seismogenesis. We found the evidence in the spatial pattern of the co-seismic ground displacement, which was well captured by synthetic aperture radar, reflecting geothermal anomalies there. A dynamic forward model including the inter-seismic deformation of DSZ naturally reproduced this displacement pattern without kinematic inversions and consistently explained other independent observations. This finding should make breakthroughs in observational and theoretical studies of earthquake generation.