Guptill injured his right hamstring during training, a separate injury to the one on his left leg that ruled the opening batsman out of the Bangladesh T20 series in January and one-day matches against Australia earlier this month.
Auckland wicketkeeper-batsman Glenn Phillips will make his international debut as Guptill's replacement for Friday's T20 match at Eden Park, the team said on Wednesday.
Dean Brownlie takes Guptill's place in the ODI squad for the first two fixtures of the five-game series.
Selector Gavin Larsen said the 20-year-old Phillips earned his selection on the strength of his domestic form.
"Glenn was outstanding for Auckland at the top of the order ... and proved an extremely exciting player," he said in a media release.
"He bats with power; has shown he can clear the rope, and gets a deserved opportunity to showcase his skills on the international stage.
"Glenn will play as a specialist batsman only, with Luke Ronchi still taking the gloves. Playing in his home city, it will certainly be a big occasion for Glenn."
(Reporting by Ian Ransom in Melbourne; Editing by Greg Stutchbury)
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