Team manager Lindsay Crocker said opening batsman Michael Papps had been named in the side for the Test, starting at Headingley on Thursday, after McMillan was ruled out after practise on Wednesday.
McMillan broke the little finger of his left hand for the second time in the tour during the four-day match against Leicestershire last week.
Captain Stephen Fleming was also named in the side, despite missing practice on Wednesday with an ear infection, although batsman Mathew Sinclair has been placed on standby in case Fleming does not recover.
New Zealand, who lost the first Test at Lord's by seven wickets last month, face an uphill battle to square the series in Leeds.
All rounder Jacob Oram will not bowl at Headingley after failing to recover from a side injury he picked up on the final day at Lord's. He will play as a specialist batsman.
Strike bowler Shane Bond, who missed the first Test because he lacked match fitness after spending more than a year out of the national side with a stress fracture in his back, was ruled out earlier.
The New Zealand side, who lacked penetration at Lord's will go into the match with only two specialist pace bowlers in Daryl Tuffey and Chris Martin.
All rounders Chris Cairns and Scott Styris will be expected to fill the third and fourth seamers' roles after Oram's injury with Daniel Vettori the only recognised spinner.
Papps is likely to open the batting with Mark Richardson, who scored 93 and 101 at Lord's, with Fleming dropping down to his usual number three position.
If Fleming fails to recover, Sinclair will slot into his position in the batting order.
Team: Stephen Fleming (captain), Michael Papps, Mark Richardson, Nathan Astle, Scott Styris, Jacob Oram, Brendon McCullum (wicketkeeper), Daniel Vettori, Chris Cairns, Chris Martin, Daryl Tuffey.
