3months stay 6months visa.NHI/pension system?

As a part of my PhD program in Italy, I will spend 3 months in Kyoto University. The university officially enrolled me for 3 months (October - November - December).
However, during the procedures for the CoE, even if we (the University and me) asked for a 3 months stay, the Japanese Immigration wrote "6 months" on the certificate of eligibility. I don't know if they thought of doing me a favor or what, but they make my life just more complicated.
Today I contacted the consulate in Milan and they told me that - because of that - they have to release a 6 months visa, and they cannot release a 3 months one.

The difference is that a simple 3 months visa would have avoided the residence status process. Now, with a 6 months visa, I will have my resident card, I will have to register my place of residence and enroll for the National Health Insurance at the local City Hall (in my case, Uji City office). According to the University, I also have to enroll for the National pension system.

The fact is that I want to stay just for 3 months and I have also already bought my return ticket for December 23.

Now, obviously I have to register my place of residence, but I was wondering if there is a way to avoid the enrollment to the NHI and - especially - the National pension system.

As a PhD student, I am already paying the Italian pension system (about 100 euros per month) and I am not interested in having a pension in Japan (and for 3 months, I think it is just a waste of time and money). Always according to the University, as a non-regular (non-degree seeking) student (research student), I can file for the general exemption system. However, I find no information on the matter on the official website.

As for the NHI, I would prefer a private insurance which can grant me a little more. Am I really obliged to enroll?

In case I have to enroll to both of them, can you tell me if there is a procedure to notify my departure before the expiration date of the visa, in order to stop paying for NHI and National pension system? The last thing I want is to have problem with the Japan immigration...

Thank you in advance for all the help you can give me.
I have tried all manner of things to avoid this, but the consulate is firm.

If you are an Italian citizen and hold the Italian passport, you are allowed to stay and study in Japan up to 90 days without getting a visa due to visa waiver policy between Japan and Italy. The policy doesn't require you to register and pay NHI and pension in JP.

The university required the college student visa. I had no choice on the matter. Otherwise no University housing for me. That's what they said to me back in spring.

Anyway, I have already the certificate of eligibility so I think it's a little too late to enter as a "tourist" .

If you pay JP pension fund for at least 6 months, you can be asked to refund apart as you leave JP. However, if you stay for 3 months, the refund system doesn't work for you.
All residents in JP include foreigners are compulsory to join in NHI and pension fund. But, if you have financial difficulties to pay off those expenses, the local city office may allow you to exempt NHI and pension payments. This decision is made by the city office. Not Kyoto University.
I suppose you stay in an international student house of Kyoto University which locate either Kyoto or Uji city. You go and visit either Kyoto or Uji city office NHI and pension department, and explain your financial difficulties there. I think some of Kyoto university students do the same thing so that Kyoto or Uji city office understand your explanation.
If you are a JP government scholarship student, you can not escape that.

Thank you for your reply!

I don't have financial difficulties. I receive a scholarship from my (italian) University.
Anyway, I did some research yesterday and I found out that:

- the income is calculated on income in Japan (for me 0)
- scholarship is not income (and again, I don't receive any scholarships from Japan)
(source: http://www.nagasaki-u.ac.jp/ryugaku/e/cis/kenko_1.html)

That means that:

1) As for the NHI, I can receive a student 70% discount and pay very little. I can manage it, I can even pay for the entire 6 months period.
2) As for the National pension system, "those students, such as auditing students and researchers, who are not enrolled as regular students are not eligible for the Student Payment Exemption Scheme described above, but can still apply for exemption from National Pension contributions, through a system that awards partial or total exemption based on income from the previous year (or 2 years before if applying between January and June). Apart from those students who worked in Japan previous to studying, the majority of students are eligible for exemption."
(source: http://www.nagasaki-u.ac.jp/ryugaku/e/cis/kenko_2.html)

So, again as a student with 0 income in Japan, I can apply for exemption from National Pension contributions.

I will ask to the Uji city office anyway. The problem is that I cannot speak Japanese fluently (I speak very broken Japanese), so I have to ask to a native speaker to accompany me...
I really wonder why foreigners stuff are dealt by people who cannot speak (at least basic) English. Sigh.

do you have a health insurance which is valid in Japan ?

Before discovering all this, I was thinking of a private insurance like coverwise, columbus... stuff like that.
However, if I have to apply for the NHI, they seem to be pretty useless for me right now, aren't they?

that's right.
all Japanese join health insurances, either of National health insurance or employer's related insurance.
because you don't have an income in Japan, your insurance fee is minimal. may be a few thousand yen per month. it will be cheap.

if you join national pension system,
if you unfortunately get injured to be a handicapped person, you can get some pension forever until dying.

@ken

even if I won't live in Japan anymore?
Because I will leave Japan for good after December.

And in Italy (and in EU in general) I am covered by the Italian health system for free and I am already paying for (my) Italian pension system.

Really, I don't understand the point in paying a pension system if I don't want to live in that country and I want stay there just for 3-6 months...

actually, address registration, health insurance, and pension are proceeded at the different sections in the same city hall building.
generally, you are requested to join pension system simultaneously, if you join health insurance.
officers worry about that you become sick with no health insurance when you are in Japan
if you have a health insurance for foreign tourists, and you think it is enough, you may not necessary to join national health insurance. (actually, Japanese, who are hired by companies, join company's health insurance system, not join national health insurance.)
please confirm how your health insurance system works in Japan.

I don't have any problem with the NHI.
However, as a foreigner with a short stay visa, I would prefer to have the choice and - in case - the right to choose a private health insurance. It was not my plan to enter in Japan without any health insurance (I am well aware of the risk of not having any insurance), but I would prefer a private health insurance (such as coverwise, just to give an example). It costs much more than NHI, but it covers also important matters for a foreigner which are NOT covered by NHI (e.g., if someone in my family in Italy gets very sick, they cover my travel expenses).

The pension system is a different matter. It's ok (and important!) if I want to spend my life in Japan, but this is simply not my plan. Again, I think it should be a choice, not an obligation, especially for a foreigner with a short stay visa.

Obviously, that's just my opinion biased by the fact that I am a foreigner.

You are free to take any private inurance you like, but you still have to enroll and pay into the national health insurance scheme. That's how it works in every civilised country (Italy very much included). Don't like that? Go to the US.

Are you planning on coming back to Japan in the future, or is this a one time trip type thing?

Also, what paperwork does your university require in order to enroll for those three months as a student? In other words, do they require your enrollment into the pension system as a prerequisite for enrollment?

@scarreddragon
As a tourist, probably. To live/work, very unlikely.

I am already enrolled to the university. It was an important step in order to get the visa. They ask me to do that AFTER the enrollment.

Anyway, I talked with my Japanese professor and she is helping me to understand what to do/ not to do. I think I will enroll to the NHI and just ask for exemption to the pension system.

If you don't want it, just don't sign up for it. It's that simple.