Coltman injured his ribs against Tasman last Friday night but it was hoped he would be right for the match against Auckland.
However, he is still in a fair amount of pain and has been replaced by Dunedin hooker Sam Anderson-Heather. Coltman has not broken his ribs but he is also in doubt to play against Wellington next Thursday night.
It will be Millar's debut as captain of Otago although he has captained his Pirates club side for the past two years.
Sekonaia Pole comes into the reserves and will make his first-class debut should he get on to the field.
It is a chance for Anderson-Heather to impress. He has played 36 games for Otago although the bulk of his appearances have come off the bench.
Injury has limited his involvement this season in club play but he is fit and healthy for the Otago season.
In other changes in the pack, Mika Mafi comes back in at No 8 and Naulia Dawai starts his first game of the season on the blindside flank.
Mafi replaces Charlie O'Connell, who injured his calf while scoring a try against Tasman and aggravated it further at work on Wednesday.
Promising flanker Dillon Hunt comes into the reserves and, like Pole, is in line to make his first-class debut.
Lock Josh Dickson is also in the reserves, getting a rest after a torrid start to the season.
In the backline, Michael Collins gets a chance at second five-eighth after some solid efforts off the bench in the past two games.
Matt Faddes moves into centre, swapping places with Jayden Spence, who moves to the right wing.
Tony Ensor comes back into the squad at fullback and Peter Breen drops out of the match-day squad.
It looms as a tough game for Otago with Auckland looking ominous at times in its win over Manawatu on Wednesday night.
Otago also has to factor in the short turnaround - it is taking on Wellington just four days after its match in Auckland.
The side will return from Auckland early Monday morning and then hop on a plane just two days later to head to the capital.
Auckland showed some nice touches in the victory against Manawatu and, if left with space and time, will be very dangerous.
Auckland tore out to a big lead and, although Manawatu came back, Auckland won comfortably in the end.
Auckland was still assessing players yesterday and will not name its team until today at the earliest.
Otago v Auckland
Eden Park, Sunday, 2.30pm
Otago: Tony Ensor, Jayden Spence, Matt Faddes, Michael Collins, Jack Wilson, Fletcher Smith, Josh Renton, Mika Mafi, Adam Knight, Naulia Dawai, Tom Franklin, Blair Tweed, Hisa Sasagi, Sam Anderson-Heather, Craig Millar (captain). Reserves: Sekonaia Pole, Donald Brighouse, Aki Seiuli, Josh Dickson, Dillon Hunt, Kaide Whiting, Sio Tomkinson, Tei Walden.
