This paper estimates the parameters of the wage equation of the new economic geography (NEG) using a newly developed spatial panel model. The results show that wage rate variation across different prefectures in Japan can be explained by market potential, which is a key variable in NEG theory, whilst controlling for variation in labour efficiency. Spatial heterogeneity is particularly important in the context of Japan in part because of its complex physical geography and the spatial distribution of its principal urban centres. The paper considers the challenges associated with representing the spatial relationships between prefectures describing and implementing different approaches to measuring transport costs.