This article is a translation of the Japanese original. Where the two differ, the Japanese version prevails. Read the Japanese original（日本語版を読む）
Paying the whole of the unpaid amount and submitting a detailed 理由書 (written explanation) are both essential. But you must be prepared for strict screening, in which those steps alone do not guarantee that permission will be given. For 「高度専門職」, the fulfilment of public obligations is checked more strictly than for other statuses of residence, and applying while amounts are still unpaid carries, as a rule, a very high risk of denial.
A friend living in Japan on 在留資格「高度専門職1号」 (Highly Skilled Professional (i)) turns out to have paid none of his pension or health insurance, and a change of status application is coming up because he is moving to a new employer.
It is a status that gives preferential treatment to people said to serve the interests of Japan, so it is looked at more strictly than an ordinary work visa.
高度専門職 is a status of residence that gives preferential treatment to people who are said to serve the interests of Japan. For that reason, unpaid tax, pension and insurance, which are duties of every resident, are looked at more strictly than under an ordinary work visa.
When you apply to change status because your organisation changes, your points are calculated again and your conduct in meeting these public obligations is screened again as well. Applying while amounts are still unpaid carries, as a rule, a very high risk of denial.
Paying everything in full and explaining it is basically the only route, and the quality of that explanation matters.
3 points: how long and how much was unpaid, whether you paid of your own accord, and how high your points are.
Do not take the optimistic view that "it will be fine as long as I pay it all". You need to see the present situation for what it is: one step away from losing your status of residence. If this change of status application is refused, recovery may in some cases require a record of proper payment measured in years. The first thing to do is to pay everything in full as soon as possible and start building that record.
Applying while amounts are unpaid carries, as a rule, a very high risk of denial. Noticing the problem yourself and paying everything in full before you file the application is treated as showing at least a minimum of good faith.
Paying in full and submitting a detailed 理由書 (written explanation) are essential, but they do not by themselves guarantee that permission will be given. The decision is an overall one, taking into account how long and how much was unpaid, whether you paid of your own accord, how high your points are, and so on.
3 points: a clear account of your previous form of employment and of your present situation, a logical explanation of how the misunderstanding arose, and concrete steps to prevent it happening again, such as setting up a direct debit from a bank account. An explanation that says only "I did not know" is not enough.
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This page is a translation of the Japanese original. Where the two differ, the Japanese version prevails.