Effective on 1st June 2008, Japan will implement new regulation when you bring hand carry money exceeding JPY1 million (approx. US$10,000) or equivalent amount of cash, traveler's check, bond, securities etc. , you need to declare the amount in Customs application form. This is in order to monitor illegal money laundering activity which is regulated world wide.
Both export (bring out) and import (bring in) are subject to this new regulation. In addition, gold ore more than 1 kg is also applicable to this declaration requirement.
Actually this notification requirement have been implemented by FEFTL (Foreign Exchange and Foreign Trade Law) since 1998, now with amending the Customs Law, Japanese Government tighten the monitoring the hand carry more closely.
The application form will be distributed in airport, and you can download from Customs web site. It looks easy and simple to fill in.
If you fail to declare, the penalty is not more than five years of imprisonment or a fine of not more than five millions yen based on the Customs Law Article 111. Same penalty would be given if you "try" to do so.
(Source: Japan Customs web site http://www.customs.go.jp/kaigairyoko/shiharaishudan.htm )