The 58-year-old man was taking part in the 47km mountain biking event, from Glendhu Bay in Wānaka to Arrowtown’s Wilcox Green.
In a statement, the Motatapu race director and co-owner Gemma Peskett said their team worked closely with emergency services at the time, and continued to assist.
"We would like to offer our deepest condolences to the bereaved family."
The Otago Daily Times understands the man collapsed about 1.5km into the race and was unresponsive when an athlete found him.
That athlete started CPR before others came to assist, including a doctor.
It was a sad start to the first Motatapu event in three years, Ms Peskett said.
Senior Sergeant Chris Brooks said police were asking anyone who may have seen the man beforehand, or saw exactly what happened, to come forward.
"We know that there would have been competitors and supporters in the bike race who had travelled to Wānaka from all parts of the country," he said.
"So we are asking anyone - whether you are currently in the Wānaka area or have since returned home - who may have information to please let us know, so we can help get some answers for this man's family."
About 4000 mountain bikers, runners and walkers participated across six events, which included an off-road marathon an ultra run and the 56km Coronet Loop mountain bike race.
The 52.5km ultra run was won by Weston Hill in 6hr 4min, while Reef Roberts won the Motatapu mountain bike in 2hr 10min, followed by Taz Selfe in second, a split second ahead of Joshua Barley, who came third.
Amy McClintock, who just moved from Christchurch to Wānaka, won the 19-39 female category and came second overall with 2hr 46min.
That event was won by Georgina Read in 2hr 44min.
Sam Shaw won the inaugural Coronet Loop event, finishing in 2hr 42min, 16min clear of Neill Ungerer, who came in second, and Brent Miller, who finished third.
Kim Hurst was the first woman home on the Coronet Loop, in 3hr 34min, with Hannah Miller in second in 3hr 44min 35sec and Meggie Bichard in third with a time of 4hr.
In the off-road marathon, Ben Gatting was first man home in 3hr 1min, followed by Scott Hawker (3hr 17min 26sec) and Lars Winther (3hr 24min 44sec), while Ella Fry won the women’s event (3hr 41min 22sec), with Sammy Burke in second (3hr 53min 43sec) and Nikki Hill in third (3hr 55min 49sec).
