Mark Chapman and Zak Foulkes have been ruled out of the five-match series, with all-rounder Josh Clarkson and fast bowler Blair Tickner named as replacements.
New Zealand Cricket said Chapman injured his left hamstring while playing in the European T20 league last month. The organization expects him to be available for the ODI series against India.
Foulkes injured his right hip flexor during a Canterbury team training session, and no return date has been set. Head coach Rob Walter wished both players a smooth recovery and said the team could rely on Clarkson and Tickner.
The five-match T20I series begins on October 22. New Zealand will be led by Mitchell Santner and has named a 16-player squad. Matches will be played in Christchurch, Wellington, Auckland and Hamilton.
The opening game is scheduled at Hagley Oval in Christchurch. The teams will play there again on October 24 before the series moves to Wellington and Auckland. The fifth and final match is set for November 1 in Hamilton.