Mitchell Santner, who was India's destroyer-in-chief last year, was appointed as New Zealand's 32nd Test captain on Tuesday. The first Test will start on Thursday.
"Test captain Tom Latham has been ruled out of the first Test against Zimbabwe with a shoulder injury," New Zealand Cricket has said in a statement.
"Latham suffered the injury while fielding during a T20 match for Birmingham earlier this month and has not recovered sufficiently to be included in the eleven on Wednesday."
Tom Latham will remain with the squad and is likely to return for the second Test starting August 7.
Santner is also New Zealand's white-ball captain and has played 30 Tests for the Blackcaps. He will assume the role fresh off a T20I Tri-Series victory in Harare where New Zealand remained undefeated throughout the five-match series.
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"It’s hugely disappointing for Tom to be missing the first Test, as captain but also as an integral part of the team,” New Zealand head coach Rob Walter said.
“It’s never great when you lose your captain, who’s a world-class opening batter and a great team man, but that said we’re going to work really hard to have him available for the second Test.
"We’ll continue to assess and see whether a replacement player is necessary, but at this stage we are hopeful that he'll recover in time.”
Walter said the team was in good hands with Santner.
“Mitch did a wonderful job with the T20 squad in this recent series.
“He was excellent from a strategy point of view and he has a strong understanding of the game.
"Whilst the format is different, he certainly has the respect of the players and will be supported by some highly experienced Test cricketers, so I trust that he’s going to do a great job.”