I've just found these sales numbers on the official Nintendo website: http://www.nintendo.co.jp/ir/en/sales/hard_soft/index.html

Note: the numbers are from September

Now compare to the VGChartz numbers:

NDS: 

Wii: 

3DS: 

Note how the sales for NDS and Wii are already higher in September and the 3DS only is ~1Mil below with millions sellers like Paper Mario: Sticker Star and Animal Crossing: New Leaf yet to release?

How comes the software sales hadn't been adjusted when Nintendo released those numbers?

Yes they are and we demand an explanation. Especially Zelda Skyward Sword

Shipment data?

VGChartz data for the end of September can be seen here - http://www.vgchartz.com/weekly/41182/Global/

The only thing that seems highly undertracked is DS Software... But good luck finding out what/where it is.

For example they could take the missing numbers and add them to the games after a certain key, based on how much the games sold according to VGChartz. Seeing how the error already is almost 20%, it most certainly could only improve the accuracy of the sales. 

Yes, those figures are for the amount of shipped software.  The DS is off by the most because a lot of software from before VGC came about probably isn't tracked.  For example, through the end of 2007 there was 330.88 million units shipped, but VGC recorded 213.87 million.

No it wouldn't.  The software isn't uniformly undertracked.  Some games are tracked fine, some are undertracked, and some aren't tracked at all.

Arent those numbers from Nintendo shipments?

Another thing to consider is that those Nintendo numbers might contain digital sales, which VGChartz does not track.

Digital sales of DS software.... you mean piracy? :D The DS itself has no store for software.

:D

Yes they are especially certain games on the Wii U. Monster Hunter 3 Ultimate figures makes no sense especially when you compare its miiverse community to its NSMBU community in Japan alone.