Your accountant gives advice very similar to the advice of my accountant and the accountants of my friends.
Japan has, essentially, a bifurcated employment market [+]. There exist people that accept contract positions; contract positions appear to be widely used within e.g. Tokyo startups. There also exist people who would not countenance a contract position.
One of the key hiring challenges in Japanese startups is finding folks who are both a) productive and b) willing to participate in the half of the labor market that people-the-system-views-as-productive do not normally participate in. (One is not normally afforded huge flexibility in switching between these systems.)
There's also the fact that people accepting contract positions are at a significant disadvantage regarding banks if they want to get a loan to buy a house. It's considered lower status to not be a seishain.
But, on the other hand, when it comes to Software Engineering, salaries for contract positions tend to be higher and, in my experience, being a seishain or being a contract worker has no bearing on the competence of the person.
As a new (American) grad I briefly looked into working in Japan. The companies I was interested in were posting for Americans specifically, but they were still hiring people on as salarymen. The rates, even COLA-adjusted, were shockingly low. Like, top-flight companies offering bottom 10% salaries in American terms.
That whole experience has come to make way more sense as I've learned about the contractor divide, and the expectation that salaried workers will "start at the bottom".
Even at the top end, salaries in Japan are shockingly low AFAICT. Especially if you come out here to the countryside, most programmers are working for insurance companies, etc. I know people with 10 years of experience making in the 3-4 million yen (just over $30-40K USD) range. It's one of the reasons I do remote contracts.
Japan has, essentially, a bifurcated employment market [+]. There exist people that accept contract positions; contract positions appear to be widely used within e.g. Tokyo startups. There also exist people who would not countenance a contract position.
One of the key hiring challenges in Japanese startups is finding folks who are both a) productive and b) willing to participate in the half of the labor market that people-the-system-views-as-productive do not normally participate in. (One is not normally afforded huge flexibility in switching between these systems.)
+ Slightly more fractured than this suggests.