The abundance of the northern form of the short-finned pilot whale, Globicephala macrorhynchus, in the Pacific waters of northern Japan was estimated from a line transect survey conducted in 2006 and data from seven previous surveys collected between 1985 and 1997. To overcome the difficulty of small sample size and inconsistency in survey design, we used an adjustment method using multiple covariates and sensitivity analysis by considering several scenarios. Abundance estimates showed similar long-term trends among scenarios. The northern form of G. macrorhynchus was more abundant in 1985 than in 1991–2006. The annual catch of the northern form of G. macrorhynchus exceeded the potential biological removal (PBR), especially in the 1980s. Thus, the commercial take in the early 1980s was suspected as a partial cause of a serious abundance decrease. These results provide valuable information for interpreting the impacts of coastal whaling, and to develop future management plans.