I did a quick check at BCN this afternoon while writing this post, and the iPhone 3GS 32GB is listed in first place in sales (see screenshot at right), with the iPhone 3GS 16GB in second place. The 3GS was just introduced in Japan on June 26th, and the sales figures are from the week of June 22 - 28. BCN's source of data includes point-of-sale information from many of Japan's largest electronics retailers, including Amazon Japan, Eiden, Bic Camera, K's Denki, and Best Denki.
Akky Akimoto at Asiajin is providing some perspective on the numbers. It's not unusual for a new phone to jump to the top of the list as it is released. As he notes, the Sony Network Walkman was #1 in the BCN ranking of music players at one time in 2005, but for the complete year, Apple iPod had a 60% share of the Japanese market.
Still, this is good news for Apple, and as Mr. Akimoto says, "Becoming No. 1 even for a week is better than never being No. 1..."