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.

http://www.gamesindustry.biz/content_page.php?aid=29245
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.

According to the latest data from Media Create, Halo 3 is one of six new entries in the top ten, as PSP, PS2 and PS3 software sees a resurgence after months of Nintendo domination.

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)"

So Crisis Core didn't get 64k?

Somebody's numbers/estimations are a bit off.

I think Japan has two companies that track sales and their numbers vary with each other as well.

Funny, I didn't hear anyone mentioned that FFVII:CC top the chart for two weeks because "Media Create doesn't combine the sales of the two seperate Pokemon Mystery Dungeon games". Really, does it really matter which game is No.1 on the chart?

@wenlan, this is new because it is a 360 game and a shooter. Two things that don't do well in Japan.

First number of media create, the true are known friday. 

1. Halo 3 X360 59.000 59.000
2. Pokémon : Donjon Mystère Equipe d'Expédition Temps DS 55.000 440.000
3. Crisis Core : Final Fantasy VII PSP 54.000 649.000
4. Tamagotchi Connexion Corner Shop 3 DS 54.000 54.000
5. Pokémon : Donjon Mystère Equipe d'Expédition Ténèbres DS 46.000 389.000
6. Bleach : Blade Battlers 2nd PS2 31.000 31.000
7. Kanji Test DS 2 DS 28.000 28.000
8. Yu-Gi-Oh ! GX Tag Force 2 PSP 28.000 28.000
9. The Elder Scrolls IV : Oblivion PS3 27.000 27.000
10. Metal Gear Solid : Portable Ops + PSP 25.000 119.000

Wow. The best debut for a 360 game since Blue Dragon, even topping Trusty Bell. I think Microsoft spread rumors Master Chief is really Cloud. ;)

This is good stuff for Microsoft. With more people getting into the 360, Lost Odyssey should break Blue Dragon's record when it launches in December in Japan. Blue Dragon debuted with about 83k or so. I would like to see Lost Odyssey do 100k or more.

complete and definitives media creates numbers:

http://www.m-create.com/ranking/

Software: 

Hardware: 

A great win for Halo series