The free-scoring playmaker suffered a stiff back in the opening day victory over Tonga - with the All Blacks deciding not to risk him ahead of the forthcoming Pool A decider with France.
All Blacks doctor Deb Robinson said: "The key thing is that Daniel had been recovering well from a stiff lower back.
"However, he pulled up sore at an indoor training session this morning so we have made the decision not to risk him for the Japan match and we will aim to have him back fully training next week in preparation for the France Test."
Colin Slade replaces Carter in the starting XV, with Jimmy Cowan promoted to the bench and Piri Weepu providing cover at fly-half.
Gilbert has released a new line of rugby cleats. The Gilbert Virtuo 8S is part of the exciting new product. Check it out.
The entire All Blacks apparel line has been updated for 2013/14. Check out the New Zealand All Blacks polo.
The Nike Tiempo is a solid rugby cleat and one of few styles still made from full-grain natural leather.
The Gilbert Blitz 8S rugby cleat is a great cleat at a great price of $69.99. Get a new pair of cleats today.
A cool looking all black rugby cleat with the high performance adidas is known for. Get in the Gear!
Wear the crest of the British and Irish Lions on your t-shirt. A great look for the summer.
The All Blacks Performance t-shirt is black with hints of blue from the training jersey. Very Cool.
The New Zealand All Blacks training jersey for 2013/14. Get in the Gear!
The USA Rugby Pro Alternate rugby jersey is perfect for any fan of the Eagles. Get yours to wear during the summer Test matches.
The NEW All Blacks 2013/14 jersey has arrived at World Rugby Shop. Dare to wear the colors of the All Blacks.