Airborne electromagnetic surveys using a grounded electric dipole source and magnetic surveys were conducted to delineate resistivity and magnetization structures in deeper parts of tunnel construction sites in the Otoineppu area of Hokkaido, northern Japan. The survey area is mainly composed of Cretaceous sedimentary rocks, with serpentinite dykes intruded into the sedimentary rocks. The surveys covered the tunnel site and its surroundings to estimate the distribution of sediment rocks and serpentinite. The resistivity structure of deep sections and the distribution of magnetization anomalies delineated the serpentinite types and their distribution, which is useful in understanding potential geotechnical issues when excavating a tunnel.