According to Socialbakers.com, usually a reliable site that tracks Facebook usage worldwide, and Facebook itself, Facebook Japan now counts just over 3 million members.
Here is what Socialbakers says when you look up country statistics for Japan:
As you can see the stats service shows that Facebook Japan added over 500,000 users in Japan from April 4 to April 5 to reach 3,059,000 users.
I double-checked this with Facebook’s own ad creation tool, which shows this number:
As there is no way that Facebook Japan saw such a spike, there must have been a glitch somewhere (also see here and here for further discussion).
I last checked Facebook Japan’s stats in March 2011.