The match in Tokyo on November 2 will be the third official Test between the two sides after they met in World Cup games in 1995 and 2011. The All Blacks also played two matches in Japan in 1987 but those games were not awarded Test status.
What was supposed to be a mood of celebration for rugby fans in Japan turned sour after former Wallabies coach Jones said that some companies and universities were refusing to release their players for the national set-up.
"It is vital that once the players hear this announcement that they start preparing like All Blacks," Jones was quoted as saying by Kyodo news agency.
"We need every day we can to prepare to take on the best team in the world. But some of the companies and universities are not releasing their players (for next week's national team camp)."
The coach said the attitude of the concerned clubs could hamper Japan's preparation for the prestigious match.
"Japanese rugby doesn't want to win. The only people that want to win is the national team [itself]," he added.
"I hope the companies and universities are all happy because I am not happy. The problem is their heads are hard. They are living 30 or 50 years ago. They don't want to change.
"When I come back here when I am 70 with my wife for a holiday there will still be the same problems.
"The players we have are fantastic and I know they want to beat the All Blacks, but there are some who are being stopped by the companies and universities."
The game, to be played at the Prince Chichibu Memorial Rugby Ground, will be part of New Zealand's season-ending tour in the northern hemisphere.
"The match fits in perfectly with our strategy for 2013 to not only grow our game but also to grow our leadership and depth within the All Blacks squad, and will give us the chance to give younger players further opportunities in the black jersey," All Blacks coach Steve Hansen said.
Asian powerhouse Japan have appeared at every World Cup and will host the tournament in 2019.
"We are excited at the prospect of the All Blacks returning to Japan ... and we hope this Test match will provide a further boost for rugby in Japan ahead of rugby World Cup 2019," NZRU chief executive Steve Tew said in a statement.
The All Blacks recorded a 145-17 victory over Japan during the 1995 World Cup and then beat them 83-7 during the 2011 global showcase.
The Japanese beat both the United States and Canada in this year's Pacific Nations Cup and recorded their first win against Wales last month, beating them 23-8, though the Six Nations champions had 15 of their leading players on duty with the British and Irish Lions in Australia.
"The history of matches between the All Blacks and Japan hasn't been in our favour, but we have changed history once by beating Wales this year and we want to change history again when we play against the All Blacks," Japan coach Jones added.
"Every player who gets the chance to play against the All Blacks must be preparing to win against them," the former Wallabies coach added.
"It's not only a physical challenge, but also mentally we need to play a game that really makes the All Blacks think."
The All Blacks will also play France on November 9, England on November 16 and Ireland on November 23 on their end-of-season tour.
Their next match is against Australia in the southern hemisphere's Rugby Championship in Sydney on August 17.
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