Cycling New Zealand Chief Executive Jacques Landry said in a statement that the investigation's findings have led to the immediate resignation of High Performance Director Martin Barras.
"Cycling New Zealand has taken swift action following a breach of its Code of Conduct at the Tokyo Olympics," Landry said.
"After the Games team returned, I became aware of a possible integrity breach that had occurred during one of the cycling events.
"I immediately carried out a preliminary investigation. That led me to alert the New Zealand Olympic Committee (NZOC) which has jurisdiction over the New Zealand Team at Olympic Games. They then undertook an independent investigation which found that both its and Cycling New Zealand's Codes of Conduct had been breached," he said.
"As I result, I initiated discussions with the High Performance Director Mr Martin Barras."
While Landry said Barras was not directly involved in the incident, as Director he was ultimately responsible for the conduct of the New Zealand Cycling Team at the Olympic Games.
"He has therefore tendered his resignation, which I have accepted."
Mr Landry said that his organisation is providing support to the athletes involved because this incident is being made public.
"Out of respect for the participants who took part in the investigation under conditions of confidentiality, no-one at Cycling New Zealand is able to make any further comment on the matter."