@ilovejesusandgod
are the 3-5%, 10% and approx 10% respective rates based on taxable income minus both the personal exemptions (¥480,000 / ¥430,000 for residence tax)
The deductions from net income to produce taxable income are different for all three taxes, and all three are different to national income tax. I'm not going to list the dozens of possible deductions and say which taxes they each apply to, especially since there can be variations in local tax calculation methods between prefectures and municipalities. NHI calculations, in particular, vary enormously between municipalities.
In general, however:
- NHI premiums are based solely on your net income minus the 430k basic deduction. No other deductions are recognized. (Though the blue-form deduction, for example, is technically a business expense, so it does reduce your net income for NHI purposes.)
- Residence tax allows for most of the same deductions from net income as income tax, but with different amounts in many cases (e.g., a 430k basic deduction instead of 480k).
- Business income has its own separate deduction structure, as described at the page I linked. Most significantly, there is a 2.9 million yen deduction applied to the taxpayer's total business income.
income tax bracket exemptions (e.g ¥427,500 in the 3.3-6.95m bracket)
I'm not sure you've understood what those "exemptions" are. The 427,500 yen amount, for example, is not an exemption, it's just the number you need to use to quickly simulate the application of marginal taxation.
The "proper" way to apply Japan's marginal income tax rates to an income between 3.3 million and 6.95 million would be to take 5% of 1.95 million and add that to 10% of (3.3 million - 1.95 million) and add that to 20% of the amount in excess of 3.3 million. But the same result can be reached by just taking 20% of the total amount and subtracting 427,500. They are two different ways of producing the same result, with the second way being much faster (though less intuitive).
There is no need for any such shortcuts when applying tax rates that are not marginal. And none of the local taxes you are discussing use marginal tax rates.
Are health insurance and pension contributions tax deductible for self-employed persons in the same way as business tax?
Yes, but not in the same way. Health insurance and pension premiums are deemed to be paid by the individual in their private capacity, not in their capacity as a business operator. So they are not deductible business expenses. However, health insurance and pension premium payments are
tax deductible for individuals.
are there any other major significant tax strategies to be aware of?
None that come to mind. But what I would say is that professional advice can be extremely valuable when starting a new business. New businesses have a high chance of being audited, and a professional can make sure you are on the right path from the beginning.