My experience was that the ATM's I used didn't charge a flat fee - it was something like 100 yen for 100 USD and 200 yen for 200 USD. Don't remember which ones I used, but the few I used were all the same. This was in Tokyo city
A lot nicer than the Thai ones that charge $7 usd whether u withdraw $1 or $100 (and you can't really max out b/c most have a limit of around $300-500 usd depending on the bank which you don't know until far into the transaction )