The 30-year-old smacked 104 against the West Indies in the third and final T20 match at Mount Maungauni.
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Munro, with previous centuries against India and Bangladesh, moves ahead of four players, including the West Indies' Chris Gayle, on two T20 centuries.
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He also leaves Indian power-hitter Rohit Sharma behind to achieve this mammoth feat.
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His rollicking 104 off 53 deliveries included 10 sixes and three fours.
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Munro stitched a brilliant hundred run stand with opener Martin Guptill for the first wicket
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New Zealand's Colin Munro became the first player to hit three centuries in international Twenty20 cricket.