That is going to happen to at least some point without your having to do anything. Google uses a load-balancing mechanism to load different Google sites according to the audience. It would not make sense for a data center to serve sites and pages that a portion of the world is not looking for or in a language that is not understood. The .com site will have a wider reach while the .jp site would be more regional.
There are two major criteria for this: one, language; and two, interest based upon search history. From time to time, Google will taste a sites performance in a locale to see what interest there may be. Mostly, however, the outcome is predictable based upon search history for a locale and any sites semantic profile. It is simple math at that point. But because populations do change over time, occasional tests are made to see if anything moves the needle even it is just a little.
You can look into GEO targeting using language and other criteria such as using schema.org mark-up for company location and so forth. You can possibly use, at least for the .jp site, Google Webmaster Tools to indicate the desired audience. I would save this option for the last step making sure that it is a necessary step first. Google is very good at what it does. I would see what happens before getting too carried away. There are plenty of GEO targeting questions and answers here to get you started. But I stress going natural first and only fixing a problem if it exists.