Neither he nor his wife should be permanant residents after so long away, so my guess is they applied for a business manager visa. If I remember correctly, the main component of this is a fully flushed out business plan, and a certain amount of capital beyond startup costs to keep the business afloat (starting around 10,000 USD). Then, the business must turn a profit after the first 12-18 months to be renewed. if I remember correctly. There are also some rules about employing Japanese citizens, but I think it depends on the size of the business.
The only other possibility is that he is simply employed by somebody else who is startig a nursury and wants him to run it. Seems unlikely.