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Afaik the employer does not have to pay the employer's share of the social security fees by enrolling them into the pension system if the teachers do not work a certain amount of hours per week (Part-time employees must enter the pension system if their working hours and days exceed three-quarters of the working time of a full-time worker in the company). There is a minimum contribution of 15020 yen per month though, although I have no idea how the Kokumin Nenkin enforces that. From time to time the weeklies report that a tarento or politician has been slacking on his contributions, although I think that the My-number-system will change that.
It's possible for some nationals to receive a lump-sum payment of their fees when leaving Japan. After doing some paperwork it's also possible to add the contribution period in Japan to one's contribution period to the German national pension system, although I'm not familiar with the details. There may be similar bilateral treaties with other countries which also have a national pension insurance.
Immigration would never issue a work visa to a person being paid less than 3,000,000 yen. So you are referring to somebody who is a permanent resident or has a marriage visa, or a person with a work visa that has a 2nd job.
Yes, funds you put into the Japanese pension system is transferable to social security plans of other countries. However, usually when you are leaving Japan and your visa has expired. You can't do it while your Japanese visa is valid or has any significant amount of time on it. You must pay into the Japanese pension system, then when or as you are leaving, attempt to withdrawal or transfer the money into another social security plan.
My understanding is that immigration focuses on taxes, then considers your health and pension relative to your pay and job. There appears to be the assumption that the company you work for will take care of this, because they are offering this as required by Japanese law. So immigration wouldn't look into this, unless they suspect something. And if they investigate you and you have not paid into the Japanese health and pension plans, then that can cause problems in getting your visa renewed or permanent residency. Keep in mind that people under marriage visas is a different situation than those under work visas, because immigration will look at your spouse. If you are married, they are looking at if your spouse is paying health and pension, and total household income of over 4,000,000 yen.
For example on how a foreigner can have a problem. If you apply for permanent residency from a work visa, but have never paid health and pension plus have a relatively low salary than the application can be denied. Remember, paying for health and pension is a requirement for Japanese, so nobody should think that a foreigner trying to become a permanent resident would be exempt.