Hello intrcessr83,
You have hit on one of the most interesting questions in missiology (the study of missions). I am currently back in Seattle for about a month after being in Tokyo for three months as a short term missionary, I'll be heading back there at the end of September to serve in a small Baptist church doing student outreach.
At the University of Washington I got a history degree in the history of Japan and Japanese politics. Having studied Japan extensively and been there as a missionary, I would say that there is no easy answer, there are many reasons for the lack of Christian converts in Japan, I'll do my best to explain what I see as some of the most important factors.
Some people may not know, but Japan is the largest unreached people group in the world. Less than one percent of the Japanese population are born again Christians. Japan's geographic neighbors have been amazing harvest fields in the last two centuries. South Korea boasts the largest percentage of Protestant Christians of any Asian nation and is actively involved in evangelization and missions. As much as 15% of China's 1.3 billion person population are part of the underground and visible church according to some Communist Party statistics and Western estimates.
Why is it that Japan, a country with over 120 Million people, has less than 1 million Christians, even though evangelization, mission activity and proselytization have been legal in the country for over 140 years?
The first and most important factor is that Japan is a Satanic stronghold. If I were writing an academic book on this subject I would probably list this as a factor, but probably not so prominently. However, it only takes a short time in Japan to recognize the signs of spiritual oppression and darkness everywhere. This nation has been particularly singled out by the armies of the enemy. We need to be praying down these Satanic fortresses.
The Japanese animistic religion called Shinto teaches that there are 8 million demons which inhabit the nation of Japan. I actually do not doubt the truth of this -the Shinto religion is all about warding off demons with incantations, chants, trinkets and charms. However, we know the only one who can give us victory over the enemy is Jesus, and without Him we will be at the mercy of the devil and his minions.
Now there are many social reasons. Partly due to their worldview which is based so much on their Shinto and Buddhist upbringings, it is difficult for them to come to Christianity, but there are also very strong currents of atheism and materialism which are just as powerful.
One valuable way to think about it is from the standpoint of the parable of the four soils. As we have already discussed, the major problem with the Japanese is demonic dominion. This is like the seed that was cast upon the edge of the road... it gets eaten up by the birds of the air.
Secondly and thirdly there are the rocky soil and the thorns. Because of the native religions and culture the seed may be planted, but the roots never go deep and they do not grow. And because of the culture of suspicion over religion and blatant worldiness, the thorns also choke the gospel message.
I could go on about this topic for hours, we could look at the history of Japan, because there were periods in Japanese history when the Japanese were more receptive of the Gospel, and we can explore the reasons for it, but unless you are interested in missions work in Japan or deep study of the Japanese people they wouldn't be worth diving into here.
The one thing that you should learn from all of this is that the Japanese people need your prayer, they need prayer for a breakthrough. No door is closed that God cannot open. Pray for missionaries to go to the field, pray for Japanese believers to boldly witness to their neighbors... the most powerful weapon we have is prayer.