The pdf file above contains a list published by the Ministry of Justice of innovative business and research that the Japanese government considers to be important. This list is used to determine whether a company or organization is eligible for points.
In other words, you can’t receive points just by saying that your company is doing something innovative, only if you are involved in a project or research designated by the Japanese government.
On the second page of the list in this pdf file, you will see that the names of various projects are listed in Appendix 2 (related to Article 1).
First, you need to check this list to see if your company is involved in any of these projects. Of course, the pdf file is all written in Japanese, so I don’t think a foreigner who is planning to apply could make a decision about it on their own, so it would be a good idea to consult with your company’s human resources.
For your reference, I have the impression that in many cases, academic institutions such as universities fall under “Grants-in-Aid for Scientific Research”. Also, if your organization belongs to a venture company that is expected to expand in the future, it may be a company selected for the J-Startup Program.