I have been working on SMEs for a while, and as far as I know (from having interviewed officials at the statistical bureau as well as the SME Agency in Japan), the term enterprises (kigyo) differs from establishments (jigyosho) or company (kaisha). Any given enterprise can have one or more establishments.
Companies are a subset of enterprises.

Japanese data on SMEs often use establishments as the base unit and are then agglomerated into enterprises.
In the immediate post-war period, the vast majority of SMEs had just one establishment, thus data was collected per establishment. In 1963, there were roughly 3.99 million establishments, peaking at 6.64 million establishments in 1991 before declining back down to 5.80 million establishments (making up 4.19 million enterprises, a 12.8% decrease) in 2009.

Kay Shimizu
Assistant Professor
Dept of Political Science
Columbia University