I know it's slightly different than on this site but Media Create doesn't combine the sales of the two seperate Pokemon Mystery Dungeon games so in their charts Halo 3 came out on top.
Matt Martin 09:10 (BST) 04/10/2007
"Microsoft has scored a number one hit in Japan with Bungie's Halo 3 taking the top spot after selling 59,000 units in its first week of release.
The performance will no doubt please Microsoft, a company that has struggled to gain a decent foothold in the region despite signing up respected Japanese developers to deliver titles that specifically cater to the market.
Bleach Blade Battlers 2nd for the PS2, Yu-Gi-Oh! Duel Monsters GX for the PSP and Elder Scrolls IV: Oblivion for the PS3 all debut in the top ten for the week ended September 30.
Also entering the charts this week are Tamagotchi DS and English Test 2, also for Nintendo's handheld.
The top ten best-selling games for Japan follow:
1. Halo 3 (Xbox 360)
2. Pokemon Mystery Dungeon: Toki (DS)
3. Final Fantasy VII: Crisis Core (PSP)
4. Tamagotchi DS (DS)
5. Pokemon Mystery Dungeon: Yami (DS)
6. Bleach Blade Battlers 2nd (PS2)
7. English Test 2 (DS)
8. Yu-Gi-Oh! Duel Monsters GX (PSP)
9. Elder Scrolls IV: Oblivion (PS3)
10. Metal Gear Solid Portable Ops + (PSP)"