I'm not an expert on the topic but some Japanese have darker skin for the same reasons black people have dark skin, I think it's the case for some who live in Okinawa (watch "Okinawa de Suki ni Natta Ko ga Hougen Sugite Tsurasugiru" if you want proof of that) and I hink thi genetic trait also appears on peoples who worked in the rice fields from generations.
In any case don't quote me on that, but there are darker skin japaneses.