The men's race, won by Tirau's Jim McMurray, was much closer, with seven minutes separating the five fastest finishers.
Kelly (36) finished the 125km course - which was correctly measured this year after last year's course was found to be short by several kilometres - in 5hr 46min 36sec, about 30 minutes slower than the record she set last year.
Her nearest rivals, Georgie McLean, of Clyde, and Natalie Whyte, of Wanaka, finished more than an hour behind.
Kelly was one of just 17 athletes, and the only woman, to break the six-hour mark.
She was 12th overall.
No-one broke the five-hour mark.
The open men's defending champion, Marcus Roy (Invercargill), was fourth in his category and sixth overall.
He was almost an hour slower than his time last year of 4hr 33min 12sec.
The representative New Zealand mountain biker was a late entrant and many of the 640 competitors did not even realise he was on the course until they had finished.
The open men's title was awarded to Brent Miller of Christchurch, who finished in 5hr 7min 36sec, but Miller was actually beaten to the finish line by 10 seconds, courtesy of overall winner McMurray.
The former champion on the 340km Round Lake Taupo race had entered the veteran male (aged 40-49) category.
The race for third overall was close, with Wanaka's David Drake finally holding off Queenstown's Mark Williams and Alexandra's Geof Blance by about 30 seconds.
