Centre Harumichi Tatekawa missed training on Monday as he was in hospital getting treatment for a knee injury, while flyhalf Kosie Ono was absent because of family reasons.
With head coach Jones missing Saturday's match after being hospitalised by a mild stroke earlier this month, strength and conditioning coach John Pryor said the injury concern was a headache the 'Brave Blossoms' could do without.
"We are hopeful he can play Saturday," Pryor told Japanese media on Monday of Tatekawa. "It's not as if we need a couple more challenges thrown at us."
Assistant Scott Wisemantel is standing in as interim coach for Japan and said the loss of Jones for the match has had an effect on the squad.
"There is obviously some trepidation as Eddie is not here," the Australia said after Monday's training session.
"But it is time for us to evolve both as a training staff and a playing roster. Eddie is still very much the boss but he is just not with us."
The match at Tokyo's 25,000-seat Prince Chichibunomiya Stadium will be just the third between the teams and the first since the All Blacks recorded a 83-7 win over Japan en route to winning the 2011 World Cup on home soil.
The first encounter was a horror show 145-17 defeat for the Asians at the 1995 World Cup.
New Zealand enter the clash on a 10-match winning streak having retained the Rugby Championship title earlier this month and have only ever lost to six sides - Australia, England, France, South Africa, Wales and the British and Irish Lions - in 110 years of playing tests.
"If you look at teams in the top 10 in the world, the likes of Ireland, Scotland, Samoa and Argentina have never beaten the All Blacks. That gives us a benchmark," Wisemantel said.
"Saturday's game is all about knowing where we stand in terms of the world rankings."
New Zealand coach Steve Hansen is taking a squad missing nine first teamers to Japan for the clash with an eye on away matches against England, France and Ireland later in November.
Jones had said previously his squad were 'training to win' against the All Blacks but Wisemantel was perhaps more realistic at beating a side which Hansen has said will feature captain Richie McCaw and flyhalf Dan Carter.
"There's a guy called Carter and another called McCaw, so it's a good squad," Wisemantel said.
"If we are playing the best, we want to play the best and (the squad they have picked) shows respect."
Japan have been buoyed by their first win over an inexperienced and depleted Wales side in June and Wisemantel said the rare meeting with the All Blacks, the most illustrious of opposition, was a chance to show the world that the 2019 World Cup hosts were improving.
"They are the best team in the world and are going to put us under pressure. But the key point is we have to take the game to them. We can't sit back and watch," Wisemantel said.
"We want to play well and put on a really good performance so the world stands up and takes notice."
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