Wellington Free Ambulance spokesman Daniel Paul said the injury was "pretty serious."
The man was being flown to Wellington Regional Hospital by helicopter. He was hunting in Bideford, he said.
Nicole McKee, Firearms & Hunter safety programme manager at the Mountain Safety Council (MSC), said shooters had to be vigilant about safety precautions.
"Duck hunters need to ensure that their firing zone is always checked before they pull the trigger.
"They need to look at the area between them and their target, as well as beyond their target.''
Today is the first day of the duck shooting season, which lasts 4-8 weeks, depending on the region.
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In the lead up to the season, both police and the MSC stepped up publicity around safety shooting practises.