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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.shtmlImage Removed|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_2011-03-15Image Removed|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:

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Looking again on April 5th 2011, the RTTs from SLAC to the University of Osaka, RIKEN, University of Tokyo and KEK all increased with a step function from around 135ms to around 200ms around midday on the 24th March. Below is shown the RTTs for RIKEN as an example.

Routes

Comparing the routes from SLAC to RIKEN (ping.riken.jp) and from SLAC to NET.APAN.N2 (ns.jp.apan.net) on 3/11/2011, we see RIKEN has more hops and goes 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.

However on 3/22/2011 the route to RIKEN went westwards across the Pacific and the RTT was very stable with Min/Avg/Max/Stdev 131.985/132.173/132.607/0.443 ms for 148 pings. The routes to the University of OSAKA and the University of TOKYO were similar.

The route from SLAC to RIKEN on April  6th (i.e. after the step change from 135ms to 200ms on March 24th went from SLAC eastwards through Sunnyvale, Denver,Kansas, Clevland, Boston to the Avenue of the Americas in New Yor and then to Japan. This trip eastward across the US added an extra 60-70ms to RTT.