Analysis of the public records of the Japan Atomic Energy Commission and information submitted to IAEA shows that in 1999-2013, Japan has received a cumulative 4,390 kg of plutonium in MOX fuel (this does not include a 255 kg shipment from the United Kingdom in 1999, which was sent back in 2002). Of this amount, 1,888 kg has been irradiated in reactors and estimated 2,501 kg remain unirradiated in storage at reactor sites. These numbers reflect the fact that MOX with 640 kg of plutonium that was loaded in the Genkai #3 reactor in March 8-12 2011 has never been irradiated and therefore counted as part of the 2,501 kg of fresh MOX. The information submitted by the Japanese government to IAEA in its INFCIRC 549 reports under the voluntary agreement of 1997 in 2012 and 2013 did not properly account for these 640 kg of plutonium. (See also the 2010 overview of Japan's MOX program.)
The first reactor that accepted MOX fuel was Genkai-3 in November 2009. It was joined by Ikata-3 in March 2010, Fukushima 1-3 in September 2010, and Takahama-3 in December 2010. In March 2011 Genkai-3 accepted a second load of MOX fuel assemblies (which were unloaded from the reactor unirradiated in March 2013).
In addition to the reactors that already use MOX, fresh fuel is stored at Kashiwazaki Kariwa, Hamaoka, and Takahama stations.
UPDATE 11/04/2014: The entry and the summary pdf file are updated to correct the amount of plutonium in MOX that was shipped to Takahama in 2013. The correct amount is 901 kg, not 920 kg, as previously stated.