In 2011 council commissioned a sustainable and healthy tree plan to "set in place a policy to guide future day to day management of the gardens" and one resulting recommendation from the consulting arborist was to remove the frisbee course.
The arborist saw frisbees were damaging trees, especially young trees, on impact and players were inadvertently causing soil compaction when they walked over root systems.
Of the 44 submissions council received on the tree plan, all were in favour of keeping the popular course.
A representative of the Queenstown Disc Golf Club, James Smithells, gave an oral submission at the community services committee meeting on Tuesday detailing the course's merits.
"It offers a free, healthy activity in an expensive town."
After the meeting, parks manager Gordon Bailey said the arborist "had his tree hat on" and council's policy had always been to retain the course.
He said the course was "very popular" and the best compromise with the long-term health of the garden's trees was to consult with the Queenstown Disc Golf Club about ways to reduce harm to trees and the soil.
"We will work with the frisbee golf people to try and minimise issues.
"Maybe small trees that are being hit need to be removed."
Consultation would be ongoing until "we get the course right".
The public would be consulted further on the tree plan, but council would delete the option of removing the frisbee golf course.