New Laws about Transfering Money
From January 4, 2007, it will no longer be possible to send sums larger than 100,000 yen in cash by “furikomi” (bank transfer) at the bank machine (ATM). If you want to send amounts larger than that, you will have to use your bank card. The banks are trying to prevent money laundering and other criminal activities, so they are limiting the amount of money that can be sent anonymously through the furikomi system. (If you send cash by furikomi, there is no official record of who sent the money.) So, if you want to send larger amounts of money, first deposit the amount into your account and then transfer the money from your account to the recipient.
Source: Japan Times (unfortunately, you have to register to view the article)