My friend runs a company in Japan. Can I stay in his company and apply for a work visa to Japan? What are the conditions?

Yes, you have to go to the embassy to ask about the specific procedures. If it's a reverse sign, ask your friend to ask the Japanese Immigration Bureau.

You can work with him for a long time.

But if you want to come to Japan and don't work there, you must figure out what to do in the second year, because the work visa is only given for one year at the beginning, and you need your income certificate, tax certificate and employment certificate issued by the company to renew it in the second year, and you can't get the tax part.