The Ministry of Justice has announced that, as of January 1st 2011, 78,488 foreigners were illegally overstaying their visas. That total is down 14.5% from a year earlier. The number doesn't represent all illegals since some individuals will likely have entered the country unrecorded. However, it's probably a reasonable guide since illegal immigrants are around 10-15% the number of overstayers. By nationality, the MoJ details four main groups: 19,271 Koreans, 10,337 Chinese, 9,329 Filipinos and 4,774 Taiwanese. The Ministry attributes the decline to the introduction of fingerprinting at immigration in 2007. That seems an odd claim unless the Ministry can show they turned away people who planned to become overstayers. You would think the decline is more down to greater enforcement and a weak market for unskilled labour. From 2004 to 2009, the number of visa overstayers declined from 219,418 to 113,072, or nearly 50% in five years, while 2010 saw a further fall to 91,770 (nearly 19%). The Ministry is now focusing on fake marriages where a foreign national may have gained a spouse visa illegally, usually through marriage brokers run by criminal gangs.
Following the earthquake, tsunami and nuclear plant destruction, 2011 is going to show up some fairly drastic changes in foreign resident and visitor data trends. It will be interesting to see what happens to the overstayer figure come January 2012
Source (Japanese)