The schools represented below are a mere small fraction of all high schools in Japan (there are over 450 in Tokyo alone). Admittedly, the schools below are ones that have historically had strong middle distance programs. If you examine the schools' "best" lists in the middle distances, you will see that they would compete quite well at NCAA DI level, even though nearly all of these students are under 18.
According to April, 2011 Track and Field magazine, in the boys 5000 meter category, over 700 high school boys ran under 15:00 in 2010; of that, 100 were under 14:28. When looking at the 3,000 meter category, the results aren't so impressive until you take into account that the 3000m is normally a junior high race, rarely timed in high school except on the way to 5,000m.
The final 2010 statistics for the women have not yet come out, but likely they will be very similar for high school girls under 10:00 for 3,000m.
Whereas Dystat (http://dyestat.rise.espn.go.com/ranking.jsp) states that the US top 100 elite girls in the 3,000 start at 10:15, in Japan the top 100 high school girls would start at somewhere under 9:30.