Presently, company which have business facilities in multiple prefectures pay their corporate enterprise tax(houjin jigyouzei) in accordance with established “pro rata standards”  in each of the prefectures they are located. 

With the exception of railway companies, non-manufacturing companies pay based upon the number of locations and employees and manufacturing companies on the basis of their number of employees.

However, due to the fact that the number of employees in factories has decreased rapidly because of developments such as far-reaching robotisation of production processes in the past 10 years, the Ministry is planning to investigate whether the current levying standards are still appropriate. 

Source: Nikkei, 総務省、法人事業税の課税方法見直し　配分ルール検証 (April 20, 2015)