Junaid, who featured prominently in the Pakistan pace battery in their Champions Trophy triumph this year and in subsequent international matches as well, has been advised at least four weeks rest.
"A scan has confirmed that he has an unhealed stress fracture in his foot which requires at least four weeks of healing period," a Pakistan Cricket Board official said.
Junaid apparently suffered the injury while playing in the Bangladesh Premier League for Khulna Titans.
He complained off pain after returning to Pakistan and scans showed he had a stress fracture.
Pakistan has already lost another left-arm pacer, Usman Shinwari to a stress fracture of the back ahead of the New Zealand tour where Pakistan will play a five-match ODI from January 6 followed by three T20 matches between the January 22 and 28.
Pakistani selectors led by former captain, Inzamam-ul-Haq are due to watch the final of the Quaid-e-Azam Trophy final in Karachi from today to access the fitness of some players before announcing the final squad for New Zealand.
Azhar also had injured his knee in September and underwent treatment in England but has made a strong comeback with a hundred in the tournament.
Both will feature in the final for their domestic team, Sui Northern Gas.
In Junaid and Usman's absence, Sohail Khan and Muhammad Irfan stand a good chance of making the tour to New Zealand.
The selectors, however, appear to be inclined to include young left-arm pacer, Mir Hamza who has bowled extremely well in domestic cricket and also for Pakistan in the limited chances he has got.
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