I think there are several reasons.
By culture, Japanese people pay attention to details and make improvements wherever possible. This might lead to inventions like the blue LEDs.
Japanese scientists have been collaborating a lot with those in foreign institutions. Some of the Nobel prizes they have received are for collaborative work.
During the bubble economy, Japan had a lot of funding to spend on research. Some of the recent prizes are for work done during that time. If this theory is correct, there might be fewer prizes in future :-p