1. You Need a real Re-Entry Permit / Multiple Re-Entry Perm,it from Immigration - Valid for 5 years and can be extended under extenuating circumstances. Don't rely on the 1 Year Special Re-Entry Permit on the Departure Card. So many PRs got burned during COVID...
2. You have to go to the Ward Office and issue the Notification of Moving Out, and specify that you are moving overseas. You also need to nominate a Tax Representative to deal with your taxes while you are out of the country.
3. If you have a property, but it is rented out, it is not available for you or your family during your time overseas, you will be deemed to be not resident in Japan during that time. On the other hand, if you were to keep the property vacant for immediate occupancy any time you returned, or for some family members to remain in Japan, then they may deem you to still be resident in Japan during that time. It may be better if your wife's property was not immediately available...
4. You will probably be liable for some National Tax on your 2023 income, though you may be eligible for a refund at the end of the year if too much tax has been withheld from payroll. Youx Tax Representative should deal with your Kakutei Shinkoku in March 2024 for any refund. In any case there will be Japanese taxes due to the Rental Property(ies).
5. You will be liable for Residents' Taxes on 2022 Income.
Residents' Taxes are levied in arrears.
Residents' Taxes on 2021 Income depended on where you were registered on 1 Jan 2022, and payable from July 2022 to June 2023, either in monthly deductions from payroll, or directly by furikomi, either in one payment in July 2022, or four quarterly payments in July and October 2022, and January and April 2023.
Residents' Taxes on 2022 Income depended on where you were registered on 1 Jan 2023, and will be payable from July 2023 to June 2024, either in monthly deductions from payroll, or directly by furikomi, either in one payment in July 2023, or four quarterly payments in July and October 2023, and January and April 2024. You or your Tax Representative will need to pay those for you.
If you are not registered as living anywhere in Japan on 1 Jan 2024, you will not be charged Residents' Taxes on 2023 Income.
6. While you are overseas, you will not be entitled to contribute to your Japanese Pension, but your wife will, and it would be recommended that she pays Overseas Contributions to her pension while abroad.
https://www.nenkin.go.jp/service/scenebetsu/kaigai.html
7. You will want to be careful about when and how to transfer funds to Japan when you return, in order to reduce tax liability. It would probably best to remit funds to Japan in the year before the year in which you actually return to Japan, but you should consult a professional.
8. I know Prestia will allow PRs to keep a bank account open whilst living temporarily overseas, with some restrictions on activities, but the big banks seem to have a policy where all activities are blocked if you tell then that you are moving overseas. Prestia Global Pass Card works overseas as both a Debit and ATM Card. Others may have other suggestions.
Those are the things that immediately spring to mind. If I think of anything else, I'll update.