The specific allegations surrounding Peden include claims of bullying, drinking and an inappropriate relationship with an athlete. High Performance Sport New Zealand have confirmed being aware of the allegations and are investigating.
Peden and wife Nicholle Bailey are believed to be estranged.
HPSNZ boss Michael Scott earlier confirmed that the allegations against Peden stretch back to before the Rio Olympic Games in 2016.
He claims to have been informed of the allegations in May, as the process for Peden's exit gained momentum.
Peden's departure looks set to keep blowing gates open further up the HPSNZ chain of command as the hunt for whoever released confidential Rio Olympic cycling review documents continues.
The Herald on Sunday was told the alleged release of unedited transcripts to Peden, before they had been anonymously collated to protect athlete identities, was "not malicious but naïve". Regardless, it still represents an extraordinary breach of protocol.
Few people, including no Cycling New Zealand staff members, could have accessed that raw material.
The interviews were meant to be conducted in confidence with HPSNZ employees Hamish Carter, Eddie Kohlhase and Paul Smith.
According to New Zealand Athletes' Federation general manager Roger Mortimer, who's managed the likes of Carter, Sarah Ulmer and Mahe Drysdale, the need to produce medals at all cost has become a worrying trend over the past decade.
"Everyone involved in sport at that level wants to win. The problem is when this over-rides areas such as respect for culture, people and environments," Mortimer said.
"Sport is a privilege for anyone, isn't it?
"The lean away from people towards outcomes at almost any costs has become a real worry in so many areas," he said.
Neither Peden nor CNZ chief executive Andrew Matheson responded to requests for comment.
