Upper Clutha Rugby Club committee member Ian Brown said the club received an "indication of charges" bill for sportsground and rugby field usage.
That indicated the rugby club could face charges of up to $8000 for the use of rugby pitches during winter, he said.
"It worked out at about $380 per week for the club," Mr Brown said.
Spreading the costs among players would have meant billing every player aged 5 or more $25 a week, he said.
Mr Brown said he had contacted Ms McKissock with the rugby club's concerns and "to her credit" she came in person to discuss the issue.
Ms McKissock said a staff member had made a mistake in calculating the fee indications, and she had apologised to the club for the error.
The "misquote" would be recalculated at the standard rate all sports organisations were charged.
This amounts to $24 per field for practices and $48 for playing fees - calculated on a per day basis.
Lakes Leisure has drawn criticism from some sectors of the Wanaka and Queenstown communities for sports ground charges to schools, community organisations, and sports clubs, since taking over the management of ratepayer owned facilities.
According to Lakes Leisure policy, the recovered charges help pay for "a fraction" of the continued upkeep and maintenance of sports grounds.
The council-controlled organisation manages sports fields and leisure complexes around the Lakes District, including the Queenstown Event Centre and aquatic facilities, such as Alpine Aqualand, the arrow and the Wanaka Community Pool.
Ms McKissock's apology follows other issues faced by Lakes Leisure, including the ousting of Queenstown and Wanaka swimming coaches from Alpine Aqualand and the Wanaka Community Pool as part of cost-cutting measures and the forced closure of the Queenstown hydroslide after 69 people were injured using the slide.
Ms McKissock said it was not embarrassing "at all" to have to issue an apology to the rugby club.
A staff member had made a basic error and was "very apologetic," once the mistake was realised, she said.
