Flood sustained ligament damage to a big toe during the 16-15 loss to South Africa at Twickenham last Saturday.
Owen Farrell, whose last start was in the first test in South Africa this year, is set to replace Flood in the starting XV against the world champions.
Lock Courtney Lawes, who missed England's first three tests of the November series because of a knee injury, has also been included in the 23-man squad. Two other locks, Mouritz Botha and Tom Palmer, have been omitted.
After beating Fiji in their opening match, England have lost to Australia and the Springboks and now face a daunting match against the All Blacks who are unbeaten in 20 tests since the start of their victorious World Cup campaign last year.
"For those in Saturday's squad the message is clear - last week we went toe to toe with the second best team in the world and felt we should have won," England head coach Stuart Lancaster said in a statement.
"Now we have a chance to take on the number one side in front of a passionate Twickenham crowd, who have been fantastic throughout the Internationals, and it is a challenge we will meet head on."