High Performance Sport New Zealand will investigate the shock departure of Cycling New Zealand's sprint coach Anthony Peden after allegations of inappropriate behaviour surfaced.

Initial reports suggested Peden and CNZ parted ways due to differing ideas on the direction going forward — but according to a report by 1News on Thursday, Peden resigned after being accused of inappropriate behaviour by cyclists and others close to the team.

More than 20 staff members reportedly left CNZ since the 2016 Rio Olympics because of the toxic environment allegedly created by Peden, the report claimed.

HPSNZ boss Michael Scott said they should have done more with the information they received.

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"While I don't yet have all the facts it is clear that we could and should have done more with the information we had," Scott said.

"I will be commissioning an investigation so that we get to the bottom of this and learn from our mistakes," Scott said, adding "integrity and ethics are fundamentals of sport".

According to the report, former staff members attempted to raise allegations of Peden's inappropriate behaviour with Cycling NZ several times over the past few years.

The issues are alleged to have included bullying, drinking and Peden's relationship with an athlete but nothing was done, the staff members said.

Peden had been CNZ head sprint coach since 2013 but resigned unexpectedly on Wednesday.

CNZ chief executive Andrew Matheson earlier said Peden's departure wasn't entirely unexpected.

"It has been a tough journey through the world championships and Commonwealth Games, so it [Peden's decision] hasn't come out of the blue."

Matheson refused to comment on the reasons for Peden's resignation, merely saying "it relates to an employee-employer relationship".

Peden guided the men's trio to three titles and 10 world championship medals, an Olympic silver at Rio and 14 Commonwealth Games podium finishes, including golds in team and individual sprint and the development of the women's programme to unprecedented levels with four medals on the Gold Coast.

Requests for comment from Peden were unsuccessful.