This is the first time racing has been shortened at the event because of bad weather since 1998, when the race was called off an hour before the race ended because of poor conditions.
This year's event was held in the Whakarewarewa Forest with riders doing laps of a set course through a network of trails.
Auckland's Jared Scollay won the 12-hour race on Saturday after finishing second in the 24-hour race during last year's event.
Jude Young took out the women's race with a convincing victory.
Organisers said on the Facebook page they would repair any damaged tracks following heavy traffic on Saturday.
The Cateye Moonride dates back to 1994 in Rotorua when a 12-hour race was part of the Mad Mad Mid-Winter Festival. A 24-hour race was offered in 2002.
Results:
Men solo race:
1st Jared Scollay, 29 laps
2nd Matt Andrew, 28 laps
3rd Angus Petrie, 26 laps
Women solo race:
1st Jude Young, 20 laps
2nd Marie Davis, 16 laps
Teams race:
1st Team Magellan Strava-tard, 36 laps
2nd Team Endura Gloworm Boys, 35 laps
3rd Team Still Classy Avantip, 35 laps