Iwata said at a press conference that the company had underestimated demand for the console, which uses motion sensitive handsets to allow physical movement to be incorporated into games.
"We must do our best to fix this abnormal lack of stock," Iwata told Reuters. "We have not been able to properly foresee demand. We will do our best to offer the machine for those who are waiting."
The Wii is the best selling of the latest batch of consoles, selling more than Microsoft's Xbox 360 and Sony's PlayStation 3 put together.
However, Nintendo has been hit by excessive demand, as well as a lawsuit after defects in the strap caused injuries to players who got over enthusiastic with the physical nature of some games.
This prompted a limited product recall from the company in December 2006.