Potentially toxic algae in Lake Taupo has led to the cancellation of the swim leg at tomorrow's Ironman 70.3 event.

Instead the race will now consist of a 3km Run, 90km Bike and 21km Run.

After receiving reports from the public of algae blooms, Waikato Regional Council scientists collected a number of algae samples on Tuesday and again yesterday from five sites.

Testing overnight by NIWA scientists has confirmed the presence of potentially toxic algal species, including Phormidium, at areas within Five Mile Bay, Acacia Bay, the main lake front in Taupō, Whakaipo Bay and Kinloch Beach.

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Ironman race director Wayne Reardon says tomorrow's race will now feature two running legs and a bike leg.

Race organisers were notified of the warning at 8pm yesterday and have been working quickly to notify all registered athletes of the change, and the options open to them.

The start location will be on Ferry Road above the original swim start. Start times and waves will remain the same.

Race Director Wayne Reardon acknowledges this is not the race athletes were hoping for, but says the health of all competitors is the first priority in this situation.

"We know athlete's will be disappointed about this news, as we are. However, our team are still committed to putting on a fantastic race on Saturday, albeit in a modified format. We look forward to seeing athletes at Athlete Check in tomorrow and on the start line on Saturday."

Reardon acknowledges that many athletes' will be disappointed not to have the opportunity to complete the full course, so Iroman will also offer all athletes the opportunity to transfer their entry at no cost to any 2018 Ironman 70.3 race in Australia or New Zealand.