The Japanese government at various levels offers subsidies to support SMEs. JETRO provides an overview of the programmes in place.   

Local government incentives for foreign companies

Quite a few local government entities offer incentives especially for foreign companies to entice them to establish a business presence. JETRO provides a list of these programs.  The programs listed there are exclusively for foreign companies, there are also support programmes for which both Japanese and foreign companies are eligible.

JETRO, Incentive Programs

JETRO, Investing in Japan’s local regions

Special Economic Districts (“Tokku)

Japan also has a system of “National Strategic Special Districts”or “tokku” for short. The system allows governments in those districts to diverge from national laws and regulations and offer additional incentives to promote certain policy goals such as increased direct foreign investment. More information about these zones is available here.