There is no comparison. The Nazi Wermacht made it a policy to liquidate an entire people in the Final Solution. And the attitude of many Europeans at the time , particularly through scapegoating, had allowed the growth of Anti-Semitism to occur in Europe. Which is deplorable.
Throughout Japan's persecution of the War, the Government did not enact policies calling for the extermination of any religious group of people, nationality, or the like. Given, there were acts of brutality committed by Japanese soldiers during the course of the war, but the catalyst of such were due to desperation and the intensity of warfare. World War II in the Pacific, in its essence, was an example of Total War.