Fleming was hoping to rejoin the side for their arrival in Lahore on November 27 but the abdominal injury that forced him to miss the final one-day tri-series match against India last week will not be healed in time.
NZC doctor Rob Campbell and medical co-ordinator Warren Frost examined Fleming on Wednesday, one day after he arrived back from Mumbai with the four players (Craig McMillan, Scott Styris, Ian Butler and Lou Vincent) who opted out of the Pakistan tour.
"Stephen requires physiotherapy treatment and rest over the next three weeks to help ensure he is fit for Pakistan's tour of New Zealand next month," Frost told reporters.
The tour to Pakistan was finally rubber-stamped by NZC on Tuesday after New Zealand had received a threatening e-mail from unknown sources advising them not to play during the holy month of Ramadan.