The rescue chopper was called to the scene about 4.40pm. The on-board paramedics treated the man, before flying him to Auckland City Hospital in a serious but stable condition.
A spokesman for Whangamata Golf Club confirmed the incident had taken place, but said no comment would be made until later today.
The man was flown to Middlemore Hospital, where he was today in a stable condition after undergoing surgery, a hospital spokeswoman said.
Michael Jurisich, general manager at Whangamata Golf Club, said the man was a visitor from Auckland who had travelled to the area for the Labour weekend holiday.
"He got hit on his jaw, broke his jaw, lost a few teeth," Mr Jurisich said.
"I was speaking to his friend today who was playing with him on Saturday here and he said he's okay, in the sense that there doesn't seem to be any long-term effects."
The incident was "unfortunate", he said, saying the person who hit the offending golf ball "did not have a good shot".
"He hooked it seriously bad," Mr Jurisich said. "Normally one would expect where he was standing to be safe, but at the end of the day on a golf course you're never safe."
Two off-duty firefighters with medical training were able to help the man as he and his friend waited for an ambulance to make the one-hour journey from Thames, as there was no available ambulance in Whangamata at the time.
"We were fortunate to have a couple of paramedic firemen who were playing on the course and they helped settled the guy," Mr Jurisich said.
"It was unfortunate that there was no ambulances in Whangamata at the time, and it took quite some time for an ambulance to come from Thames, and I think things got a bit serious because the guy was going into shock."
While serious injuries were not common at the club, there had been other incidents, Mr Jurisich said.
"It's just an occupational hazard, if you want to play golf on a golf course that's the risk you take," he said.
"It's like driving a car, I suppose, if you drive on the road you've got to hope like hell that everybody else drives sensibly, according to the rules. And sometimes they don't."