The method of on-site INS position update for highly accurate AUV operation is presented. Since the localization by GPS is not available for subsurface navigation of AUV, until reaching the critical altitude below which the bottom DVL is available, positioning has to completely rely on the INS without the aid from DVL. This decreases the accuracy of AUV positioning significantly when there exist flow disturbances like sea currents. In the proposed method, deviation from the reference trajectory is evaluated right after the vehicle starts bottom tracking with DVL operation. A lattice of test interval consisting of few verification way points are installed at the entrance of the reference trajectory. On these way points, deviations in vehicle position are evaluated referring to the SSBL estimation. Uncertainty in the scattered SSBL measurement is mitigated by optimally regressed test interval. Evaluated deviation is transmitted to the AUV via the underwater acoustic communication, to update the current vehicle position in INS. Developed method was testified during the Kuroshima survey mission of "r2D4", the latest sea-cruising AUV by IIS, the University of Tokyo, to convince its usefulness in field application