In manga/anime at least, what they use in a similar manner to the "six figure salary" in the US is 10 million yen a year salary, as in that's what shallow girls in shoujo manga want their boyfriends to make. And according to https://japantaxcalculator.com/, 10 million a year salary would break down to around 550,000 yen take-home pay a month, after deducting tax, insurance, and other mandatory contributions. (Japan's effective tax rate for personal income is around 50%). That number would vary a little based on personal tax situations and the local/municipal rate, of course. So while the 530,000 yen take-home pay might look like it was an arbitrary number, I think it was based on that "10 million yen" trope.