McCaw, Mils Muliaina and Israel Dagg all pulled out of the Japan game early on Thursday citing injuries in training, a day after Carter - who had also been named in the team - declared himself unavailable with a sore back.
"There's no truth to that idea at all," coach Graham Henry said, angrily refuting suggestions that the problems may not be genuine.
"Some people have got very fertile minds. That's not the case, it's ridiculous," he fumed.
"They're minor injuries and we have taken the precaution not to play them because we don't want to make them worse, it's as simple as that. We'd be taking a risk if we played them and we can't afford to do that."
Henry has long been under fire for a controversial rotation system at the last World Cup which saw an under-prepared All Blacks tipped out of the quarter-finals by France.
Although he has pledged not to revive the practice, Henry was questioned on Thursday whether the sudden rush of minor injuries to key players before a low-level match was merely rotation in disguise.
But Henry said it had nothing to do with the fact that a week after the All Blacks play Japan they will face France in a match which will probably decide the outcome of Pool A.
The loser will play the winner of Pool B, most likely England, in the quarter-finals with the winner playing the second-placed side which looks set to be Argentina or Scotland.
But Henry said the decision to rest the quartet had nothing to do with the upcoming schedule.
"It's just that they could make those injuries worse if they play (Japan) and that's why they're not playing. It's nothing to do with not playing anybody next week," he said.
Henry added that if the same injuries occurred before the World Cup final, it's probable the players would take the field.
"If it was the last game of the tournament and you had adequate back-up you might play them," he said. "But there's six games to go and we just can't afford to take that risk."
McCaw, who was due to play his 100th Test against Japan, has suffered a minor calf strain in his left leg, Muliaina has a tight right hamstring and Dagg, who would have covered for Muliaina, has an abdominal strain.
Japan coach John Kirwan said the absence of McCaw and Muliaina would have no effect on his side but it could disrupt the cohesion of the All Blacks.
"I'm disappointed for them, obviously they've picked up a few niggles, but it doesn't change anything for us," he said.
"Things like that are probably a coach's worst nightmare. It creates disruption and certainly doesn't help your build-up, but the All Blacks have been together enough and played together enough I don't think it will affect them too much."
Hooker Keven Mealamu will now captain the side with Isaia Toeava, who was not named in the original match 22, starting at full-back.
The forwards reshuffle sees Adam Thomson move to openside flank and Victor Vito comes off the bench.
Teams:
New Zealand:
15 Isaia Toeava, 14 Cory Jane, 13 Conrad Smith, 12 Ma'a Nonu, 11 Richard Kahui, 10 Colin Slade, 9 Andy Ellis, 8 Victor Vito, 7 Adam Thomson, 6 Jerome Kaino, 5 Sam Whitelock, 4 Brad Thorn, 3 Owen Franks, 2 Keven Mealamu (captain), 1 Tony Woodcock
Substitutes: 16 Andrew Hore, 17 John Afoa, 18 Ali Williams, 19 Anthony Boric, 20 Jimmy Cowan, 21 Piri Weepu, 22 Sonny Bill Williams
Japan:
15 Taihei Ueda, 14 Takehisa Usuzuki, 13 Koji Taira, 12 Yuta Imamura, 11 Hirotoki Onozawa, 10 Murray Williams, 9 Atsushi Hiwasa, 8 Takashi Kikutani (captain), 7 Michael Leitch, 6 Itaru Taniguchi, 5 Toshizumi Kitagawa, 4 Hitoshi Ono, 3 Nozomu Fujita, 2 Yusuke Aoki, 1 Naoki Kawamata
Substitutes: 16 Hiroki Yuhara, 17 Kensuke Hatakeyama, 18 Yuji Kitagawa, 19 Sione Vatuvei, 20 Tomoki Yoshida, 21 Shaun Webb, 22 Alisi Tupuailai