The specific allegations surrounding Peden include bullying, drinking and an inappropriate relationship with an athlete, all of which were confirmed by High Performance Sport New Zealand.
As a result, HPSNZ chief executive Michael Scott has demanded answers surrounding Peden's departure.
Scott confirmed an investigation will be launched. The terms of reference will be confirmed and shared within a week.
Repeated requests for comment from Peden were unsuccessful.
"The high performance environment is all about pressure and intensity, but there is absolutely no place for bullying," Scott said earlier.
"I became aware of this in early May and immediately contacted [Cycling New Zealand chief executive] Andrew Matheson. I congratulate him on quickly taking action. What was known within HPSNZ and what was done with that information is something that will come out of our investigation.
"This will focus on HPSNZ – our people, our processes and our actions. Our role is to give athletes the best possible chance of success, and I expect this organisation to treat with the utmost seriousness anything that may be a threat to athlete welfare."
The Herald understands a wider culture of stress pervades the CNZ environment, arguably driven by HPSNZ's overarching strategy to prioritise medals over anything else.
Given the annual funding round has become directly related to podium finishes, sources told the Herald that CNZ's default position, like many sports, has been to create a "nothing to see here" façade, regardless of any issues brewing.
CNZ's funding has dropped from $4.7 million (2016) to $4.2 million (2017) and $4.4 million (2018).
Peden was understood to have employed a domineering approach, but his methods had extended beyond his contractual brief.
The decision could place the 2020 Olympic medal dreams of men's riders - Ethan Mitchell, Sam Webster and Eddie Dawkins - and women's riders – Natasha Hansen and Emma Cumming - in jeopardy.
Peden's tenure saw the programme secure three world championship titles – all to the men's team sprint - and 10 medals, an Olympic silver at Rio and 14 Commonwealth Games podium finishes.
He's not alone as a coach who had a mixture of success and difficulties at elite level.
Australia's Charlie Walsh produced numerous champions but also had endured plenty of selection controversies.
Likewise, Shane Sutton achieved incredible results with British cycling but left his technical director role in April 2016 following bullying and discrimination allegations. A review found he operated within a "culture of fear" and the addressing of "behavioural issues" was not prioritised due to the pursuit of medals.
In the original press release, Peden said his approach was not aligned to that of CNZ, which seems a colossal understatement in hindsight.
"I can't talk in any detail around that," Matheson said at the time.
"It relates to an employee-employer relationship.
"Anthony's done an amazing job and we thank him for that."
On Wednesday, Matheson said Peden and CNZ had been talking for a while about the coach's future.
Now it seems they will prepare to spend plenty of time about his past.
