O'Rourke, who suffered a stress fracture in his back against Zimbabwe earlier this month, will miss next month's Twenty20 clashes with Australia as well as short-format series against England and West Indies in October and November.
Santner, who is set to have abdominal surgery, was described as "touch and go" to face the Australians in the three T20s in Tauranga but all-rounder Phillips will definitely miss the series as he continues to recover from a groin injury.
Opening batsman Allen will also be sidelined for three months after having surgery on his right foot.
"We're really feeling for Will at the moment and wishing him speedy recovery," New Zealand coach Rob Walter said in statement.
"He's had such an impressive start to his career and so naturally it is disappointing when an injury like this comes along, but he's a resilient guy and determined to put the work in and come back stronger.
"It's disappointing to lose the services of Glenn and Finn who have played important batting roles in our T20 set up in recent time."
Walter said he would give spinner Santner, who sustained his injury while playing in The Hundred in England, every opportunity to prove his fitness to face Australia in the Chappell-Hadlee series in early October.
"Mitch is a world class player and a crucial part of our T20 side from a skills and leadership point of view," Walter added.
"With that in mind we expect to name him in our squad when we announce it in a couple of weeks' time, and from there we can assess how his rest and rehabilitation progresses following surgery, before making a call on the eve of the series."
New Zealand also play West Indies in a three-match home Test series in late November and early December.
