"Obviously the Tauranga track is not the ideal training track at the moment and is a bit hard but I think it is a combination of a few things. It could be overtraining, the track surface and maybe not enough recovery for myself.
"It is stopping me from running at full speed and I can't get through full sessions at the moment. It is frustrating because I can't say exactly what it is."
The Papamoa Surf Life Saving star recently marked his best-ever national championship performance, collecting four gold medals. His haul included the under-19 beach flags title and the rare under-19 and open beach sprint double.
New Zealand team coach Jason Pocock said: "It's disappointing that Kodi won't be able to compete in Japan.
"He doesn't want to let the rest of the NZ selection team down. But it's important for him to focus on his long-term career and make sure he gives his leg time to heal properly."
Harman has also been named in the New Zealand Youth Team to compete at the International Surf Rescue Challenge in Australia in September.
But despite this he says his major passion and priority lies on the track rather than the sand.
"To be honest I will probably start moving away from beach sprinting next season. I just feel I want to practise more on the track," Harman said. "My highest goals are to excel on the track and be the next best sprinter that New Zealand's got. I really hope I can do it so that means I will start easing out of the beach sprinting side of things."
The Sanyo Bussan International Lifesaving Cup is on Aoshima Beach, Miyazaki, Japan from July 19 to 20. Max Beattie (Omanu) and Ben Johnston (Papamoa) are in the team, with Jake Hurley (Mairangi Bay Surf Life Saving Club) replacing Harman.