The Board of Control for Cricket in India (BCCI) tweeted that first-choice wicketkeeper Wriddhiman Saha couldn't take the field due to neck stiffness, adding that the medical team was monitoring his progress.
"Wriddhiman Saha has stiffness in his neck. The BCCI medical team is treating him and monitoring his progress. KS Bharat will be keeping wickets in his absence," read a tweet from BCCI on Saturday.
The update from BCCI did not mention a particular time for Saha returning to wicketkeeping duties during the Test.
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Saha, playing in his first Test since the pink-ball Test against Australia in Adelaide last year, batted in the first innings on Friday, making just one off 12 balls before nicking an outswinger behind to keeper Tom Blundell, becoming one of the five scalps of pacer Tim Southee.
Saha had kept wickets for 55 overs on day two.
Earlier on Friday, Shreyas Iyer had struck a century on debut in India making 345. But a five-wicket haul by Tim Southee followed by half-centuries by openers Will Young and Tom Latham helped New Zealand sit on top at the end of day two.
Resuming from 129/0 in 57 overs at stumps, Young and Latham made watchful starts on day three. Bharat came into action by taking a low catch off Ravichandran Ashwin's bowling to dismiss Young for 89 in the 67th over.