OK, to reiterate what others have said above, and add some additional points.
When you have been resident in Japan for 5 years, whether you have Permanent Residence or not, you are then treated as a Permanent Resident For Tax Purposes. Then you are subject to Japan's Global Taxation, i.e. taxable on al you global assets, income and gains, just the same as US Global Taxation.
You can claim Foreign Tax Credits on both sides for taxes paid in the other jurisdiction under the US-Japan Tax Treaty.
The Tax Office can Audit you and they can go back 5 years and claim any outstanding taxes for the period with interest. Funnily enough it seems like just about the time you became liable for these taxes in Japan on your 5th anniversary.
You can go back and file, re-file or modify your tax filings for the past 3 years. The Kakutei Shinkoku at the Tax Office.
See Here:
https://www.nta.go.jp/english/taxes/ind ... /index.htm
https://www.nta.go.jp/english/taxes/ind ... 020/01.pdf
and Here:
https://www.nta.go.jp/english/taxes/ind ... oku301.htm
So, there is zero downside to applying for PR, and it means you can lose or change your jobs without fear of deportation...
Property. Up until last year, there was a very advantageous system where Japanese Tax would let you take Depreciation loses against Overseas Properties and offset those losses against your Japanese Income Tax. This was very lucrative, and could mean that if you file you may be due a sizable tax rebate on your Japanese Income Tax. Unfortunately, this loophole has been closed, and you can now only take the Depreciation Loss against the property's income.
Dividends. As a US Citizen, you would incur US Withholding Tax at 30%. This is more than Japanese Tax on Dividends and so the net would be that you would not have to pay Tax on those Dividends.
Capital Gains. You are subject to Japanese Capital Gains Tax on all overseas Capital Gains, but you can claim Foreign Tax Credits for Taxes paid overseas (in the US) on those capital gains.
https://www.nta.go.jp/english/taxes/ind ... /12007.htm
Somebody mentioned the Exit Tax.
As a Permanent Resident for Tax Purposes you are subject to the Exit Tax if you decide to permanently leave Japan. See Here:
https://www.nta.go.jp/english/taxes/ind ... /12004.htm
A Permanent Resident For Tax Purposes with assets greater than Y100,000,000 (US$ 909M) leaving Japan is taxed Capital Gains on his entire Global Assets as Marked to Market on his departure.
On Tax Returns.
The Japanese Tax Return has to files by March 14th. You have to put all you Figures Gross and then get taxed on them.
You can then use the Japanese Tax Return when you File Your US Taxes on April 14.
You can then go back ans amend your Japanese Tax Return with the Foreign Tax Credit information and they will reduce or refund the Credits.
You could go back and do this for the last 3 years. It wouldn't surprise me if you were in for a tax refund due to your rental property income.
How old are the buildings and what are they built of? Timber frame? Concrete? Reinforced Concrete? All treated differently for Depreciation.
You can claim depreciation on the structure but not the land, but not from this year on... Only back filings...
Timber frame buildings can be depreciated of 22 years, and if it's an old building you could claim accelleratated depreciation i.e. a big loss
Concrete can be depreciated of 30 years
Reinforced Concrete can be depreciated of 47 years
Note - This does reduce the Tax Basis of the property, so you will end up paying Capital Gains Tax on all that depreciation loss claimed when you sell the property...
Interior, Fixtures and Fittings can be depreciated of 15 years
Many items can be taken as an expense in the year incurred, including maybe travel back to the US to check the properties or look for new ones...
You can expense the Mortgage Interest and other expenses against the Rental Income.
And then claim that big negative number against your income to reduce you taxable income and therefore reduce the amount of tax you have to pay in Japan.
I can try and find out who my American friend in a similar situation uses to do his accounts...