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It looks the problem is in the route to Japan not within Japan itself. I wonder if the undersea earthquake has disrupted some  cables? This appears to be in line with the information from http://www.renesys.com/blog/2011/03/japan-quake.shtml and http://www.networkworld.com/news/2011/031411-quake-damage-to-japan-cables.html?source=NWWNLE_nlt_network_architecture_2011-03-15. A map of the cables from Telegeography is seen below: Image Added

Routes

Comparing the routes from SLAC to RIKEN (ping.riken.jp) and from SLAC to NET.APAN.N2 (ns.jp.apan.net) we see RIKEN has more hops and goes Eastwards via the Avenue of the Americas in NY, while APAN goes directly via Sunnyvale near SLAC and then via Pacific Wave directly to Japan. The traceroutes from SLAC to the  University of OSAKA and the University of TOKYO  are similar to traceroute from SLAC to  RIKEN.