>>530I mentioned this in
>>479, but there are many universities with programs which are taught primarily in English.
The University of Tokyo's PEAK program has one serious drawback though: they only offer two courses of study. Unless you're specifically studying Japan/East Asia or Environmental Science, PEAK won't work for you. Todai does have some other English-language based programs other than PEAK.
The University of Tokyo is also part of the Global 30 that I mentioned in
>>479 (the Global 30 is a group of thirty Japanese universities which all offer at least some programs entirely in English).
AFAIK, in addition to all of the Global 30, JAIST (JAIST doesn't have undergrad programs), ICU, Sophia, and Temple (don't go to Temple) all have English programs as well. The new Okinawa Institute of Science and Technology is also all English speaking (though they're not open to undergrads).