The 23-year-old, viewed by local pundits as a potential successor to the retired Daniel Vettori, will be replaced by George Worker in the squad for the limited overs series against Zimbabwe and South Africa.
"We feel for Mitch because he was really excited about this tour and we were looking forward to seeing him continue his development in international cricket," New Zealand coach Mike Hesson said in a statement.
"It is unfortunate but at the same time it presents George with his first opportunity ... and we are confident that he'll fit in well."
Santner impressed on New Zealand's tour of England in June, and with his left-arm spin and competent batting has been considered capable of filling the role Vettori occupied in the side for 18 years before retiring after the World Cup final in March.
The 25-year-old Worker, a top-order left-handed batsman who also bowls orthodox left-arm spin, was the leading run scorer in New Zealand's domestic one-day competition last season.
New Zealand will play three one-day internationals and a Twenty20 match in Zimbabwe from Aug. 2 before facing South Africa in two Twenty20 matches and three one-dayers.
(Reporting by Greg Stutchbury; Editing by Peter Rutherford)
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