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Gravity survey is one of the most important geophysical methods for understanding large scale geological structure and depositional basins for resource exploration. The “microgravity surveys” with the measurements in μGal, have been more commonly conducted for smaller-scale structures in the civil engineering fields. In this paper, we conduct a gravity observation in an urban area in the western foot of Mt. Fuji to confirm that the microgravity survey can delineate and depth a lava tube in a lava flow lying at around 25–30 meters below the surface. The lava tube is successfully delineated as a remarkable low-gravity anomaly that is consistent with the known location and geometry. Also, a graphical method with spatial derivatives of gravity anomalies is found to provide a reasonable estimate on the depth of the lava tube. This result demonstrates the applicability of the microgravity method for a small-scale target but with large contrast in density to the background. Combination with other geophysical approaches, including the electro-magnetic methods may enable us to define underground structures even with less property contrasts and describe changes in pore fluids by performing in a time-lapse manner.