Corporate Inhabitant taxes (hōjinjūminzei) are local prefectural and municipal taxes, paid in the prefecture and municipalities they have their offices. These taxes are computed as a percentage of the national Corporation tax before tax credits and a per capita levy, which is determined on the basis of the amount of capital and the number of employees. (Tokyo Metropolitan on basis of capital only)
Both prefectural and municipal inhabitant tax are collected by municipal governments. If you have a company located only in one of the 23 wards of Tokyo, both are charged as one Metropolitan Corporate Inhabitant Tax.
Companies should keep in mind that even if corporate income is negative, the per capita level still need to be paid.
The amount of the tax and the scale may vary in each prefecture and municipality. Please check the local administrations for more details.
Tokyo Metropolitan Government provides details on the calculation of the Inhabitants tax burden in English.