Both Germany and Japan were on the hunt for natural resources.
Land = natural resources. And in the hands of all but the most incompetent rulers, people = natural resources. The Germans put Jewish lawyers and scientists to work as menial slave laborers, deliberately under-feeding them until they died of malnutrition. That's when they weren't shooting or gassing them. The Japanese left alone anyone who wasn't actively opposing them (i.e. raising funds for the resistance, propagandizing against Japan or attacking the Japanese administration).