Japanese RFU chief Yoshiro Mori said: "I don't know why they have chosen New Zealand over Japan. The ideal of rugby has disappeared with this decision.
"Only the interests of the bigger unions remain."
However, International Rugby Board (IRB) chief executive Mike Miller said Japan, unlike New Zealand, could not guarantee packed stadiums.
Many saw this as a golden opportunity to help spread rugby to other parts of the world, with Japan's bid attracting support from a number of the sport's big names, including ex-England captain Martin Johnson and former Australian captain Nick Farr-Jones.
New Zealand also overcame a rival bid from South Africa, which was eliminated in the first round of yesterday's vote.
It hosted the inaugural World Cup in 1987, while South Africa staged the 1995 competition. Japan had been hoping to host it for the first time.
New Zealand lost the right to host the tournament in 2003 (which went to Australia exclusively) after failing to provide assurances that venues would be clean of all advertising and sponsorship not connected to the World Cup.
Its bid had drawn on the huge popularity of rugby union in the country and it successfully hosted the recent British and Irish Lions tour.
IRB chairman Syd Millar said: "I would like to congratulate New Zealand, a great rugby nation.
"We received three excellent tenders of the highest quality. Any one of the three could have hosted a successful tournament."
