November’s World Cup semi-final drubbing to England prompted soul-searching in India and talk among the cricket board of easing out senior players.
Both men remain in the one-day squad for the visit of the Black Caps. Kohli hammered 113 off 87 balls to drive a big win over Sri Lanka in an ODI at Guwahati on Tuesday. Skipper Rohit made 83.
Batsman KL Rahul and all-rounder Axar Patel will sit out the ODI and T20 matches against New Zealand because of family commitments, the Board of Control for Cricket in India said.
It did not give reasons however for the T20 omissions of Kohli and regular all-format captain Rohit.
Hardik Pandya will continue to skipper the T20 side, having done so against Sri Lanka earlier this month.
The three-match ODI series against New Zealand begins on Wednesday in Hyderabad while the first of three T20 matches takes place at Ranchi on January 27. India will then go into a home Test series against Australia on February 9.
ODI squad: Rohit Sharma (capt), Shubman Gill, Ishan Kishan (wk), Virat Kohli, Shreyas Iyer, Suryakumar Yadav, KS Bharat (wk), Hardik Pandya , Washington Sundar, Shahbaz Ahmed, Shardul Thakur, Yuzvendra Chahal, Kuldeep Yadav, Mohammed Shami, Mohammed Siraj, Umran Malik.
T20 squad: Hardik Pandya (capt), Suryakumar Yadav, Ishan Kishan (wk), Ruturaj Gaikwad, Shubman Gill, Deepak Hooda, Rahul Tripathi, Jitesh Sharma (wk), Washington Sundar, Kuldeep Yadav, Yuzvendra Chahal, Arshdeep Singh, Umran Malik, Shivam Mavi, Prithvi Shaw, Mukesh Kumar.
Test squad against Australia: Rohit Sharma (capt), KL Rahul, Shubman Gill, Cheteshwar Pujara, Virat Kohli, Shreyas Iyer, KS Bharat (wk), Ishan Kishan (wk), Ravichandran Ashwin, Axar Patel, Kuldeep Yadav, Ravindra Jadeja, Mohammed Shami, Mohammed Shami Siraj, Umesh Yadav, Jaydev Unadkat, Suryakumar Yadav.