Not necessarily. HSBC US and HSBC Japan are different banks. Same holding company but different banks. As far as I know there is no way to avoid a fee withdrawing money from a US bank account in Japan, unless it is for a large amount and you have negotiated a fee waiver with both the US bank and a Japanese bank to whom you are transferring the funds.

If you want to minimize fee, use a no foreign fee credit card and minimize the amount of cash you use. Honestly though, unless you spending 10s of thousands of dollars in Japan, the fees are not that big.