Milne, playing for the Royal Challengers Bangalore, has won a place essentially at the expense of Auckland's sharp Lockie Ferguson, who made his New Zealand debut in the season just completed.
Add in allrounder Corey Anderson, who is playing for the Delhi Daredevils, and has had injury concerns of his own, and there's a new look to the squad of 15.
''It's been good to see all three back on the park and bowling; together they add a lot of experience to our squad," coach Mike Hesson said today.
"Mitch and Adam have been running in well, and Corey has shown he'll be capable of providing an option with the ball."
The squad is otherwise predictable, with Tom Latham to provide wicketkeeping cover for specialist Luke Ronchi; five batsmen chosen, two spinners in veteran offspinner Jeetan Patel and left arm allrounder Mitch Santner, four fast bowlers and Colin de Grandhomme, Jimmy Neesham and Anderson providing the medium pace/batting component.
In a sense it is a squad chosen with the IPL in mind. Players there have been in work since the New Zealand season ended and therefore will be ready to go when the Champions Trophy starts.
New Zealand have pool games against Australia, England and Bangladesh on June 2, 6 and 9 with semifinals in Edgbaston and Cardiff to follow and the final at The Oval on June 18.
''We believe it's an exciting squad; an experienced squad, and one that has the batting power and the bowling variations to prevail in a potentially high-scoring tournament," Hesson said.
"Having four all-rounders certainly helps with balance, and the return Mitch and Adam will offer options with the new ball, through the middle of the innings, and in the death overs."
New Zealand will play an ODI tri series in Ireland, expected to also involve Bangladesh, as preparation for the trophy. Several players will be included in that in place of those trophy-bound players still involved in the IPL.
From there, a group will stay in England in case of injury during the trophy. They could included players like seamer Matt Henry, young fast bowling allrounder Scott Kuggeleijn and batsmen Dean Brownlie and Colin Munro.
New Zealand squad for the Champions Trophy in England in June:
Kane Williamson ©, Martin Guptill, Tom Latham, Luke Ronchi, Ross Taylor, Neil Broom, Jimmy Neesham, Corey Anderson, Mitch Santner, Colin de Grandhomme, Jeetan Patel, Tim Southee, Adam Milne, Mitchell McClenaghan, Trent Boult.