A vehicle travelling towards Wanaka hit the ducks after they managed to get through a fence surrounding the course.
Two less adventurous ducks remain.
Owner Richard Sullivan said he had tried to keep them on the course by installing netting within the golf course but somehow they continued to slip through.
"They go a bit crazy at this time of the year and they just do what they want."
Ducks had been kept on the course since he opened it in 2000.
Most people in the Lake Hawea community knew about the ducks, which had become something of a local attraction, Mr Sullivan said.
"It does affect me a lot, because I have raised them and seen them every day since they hatched, but there will be others in the community who will be angry someone hit them."
Local drivers usually stopped and let the ducks cross the road, he said.
"Maybe I need to get one of those duck-crossing signs like they have in Wanaka."
Comments were posted on the Hawea community noticeboard Facebook page voicing disappointment at the ducks’ demise.
Mr Sullivan said he hoped the two ducks left would produce some ducklings which he could raise.
If that failed then he would need to go through his contacts to find some.
