Hospital officials said the man remains in a stable condition and is recovering.
It wasn't the only duck hunting accidental shooting to take place on the first day of the popular season.
On Saturday afternoon, another man in his 40s, was shot in the buttocks and leg while hunting at Glenorchy, north west of Queenstown.
Queenstown police say he suffered minor injuries caused by pellets ricocheting off something.
The Wairarapa duck hunting season runs through until June 15 with the Mountain Safety Council warning shooters to be vigilant about safety precautions.
"Duck hunters need to ensure that their firing zone is always checked before they pull the trigger,'' said Nicole McKee, the councils's firearms & hunter safety programme manager.