Have you encountered discrimination or prejudices in Japan ?

[Mike Cash]

Japanese companies refusing to pay foreign workers Medical insurance and Pensions even though required by law to pay.

Unfortunately, that can tend to happen quite a lot when foreign workers are hired as foreign workers (specificially to fill jobs Japanese won't do or, more common, to save money). When one of the prime reasons a particular job may be open to a foreigner is as a cost-cutting measure, it is only to be expected that they skimp on everything they can.

There is always the option of doing what I did: Get hired even though you're a foreigner and not just because you're a foreigner. It's harder to do, but in companies which will do it it probably never even enters their mind to handle the pay/benefits any differently than they do the Japanese employees.