The holocaust took place to some extent within Germany, and German Jews/gypsies/homosexuals were taken to extermination camps. There was no equivalent within Japan itself. Japanese war crimes took place in China and Korea, a long distance geographically and cognitively from people in Japan.
The holocaust was separate from war. The Nazis wanted to exterminate certain people as a matter of principle. Japanese crimes took place in the context of war - they were carried out by soldiers in what was seen as enemy territory. A case could be made that Japanese war crimes in world war 2 were simply extreme cases of the type of crimes committed by almost all sides in almost all wars - massacres of civilians are pretty common.
But these two reasons alone don't seem to be sufficient, because the attitude to the Second World War in general seems to be totally different in the two countries, not just with regard to "crimes against humanity".
Germans seem genuinely shamed and embarrassed about the second world war and the Nazis. Even before the war ended many Germans blamed their own leaders for their suffering, rather than the Allied forces who were physically bombing and shooting them. To some extent this shame and embarassment is expressed by strict laws on mentioning Nazism or its ideas - the laws are not just for moral reasons, but also psychologically to prevent further shame and embarrassment.
In Japan meanwhile war is seen like some sort of natural disaster that causes great harm, like an earthquake or a tsunami. School children visit the Hiroshima Peace Memorial or build paper cranes, hoping war will not return. No-one seems to be blamed for the war, its causes are somehow abstract and unimportant.
I imagine the causes of this perceptual difference are rooted in the differing social and cultural histories of the countries many decades or even centuries prior to the second world war. I do not have sufficiently in depth knowledge to even attempt such an explanation.