"I want to assure all athletes and other stakeholders with whom I have worked over the years that my overarching priority has always been to support them and their success.
"I feel very sad to be moving away from sport, something I truly love and am passionate about. I hope that one day I can return, but for now I need some time away."
HPSNZ Chief Executive Michael Scott said Carter made the decision of his own accord.
"There has been no agreement or settlement between us relating to Hamish's decision to leave HPSNZ and we want to be clear that Hamish has made this decision on his own account.
"In accepting the resignation, HPSNZ would like to recognise Hamish's contribution to the organisation since joining in 2013 and acknowledge the honesty and integrity he has shown in responding to the report by Michael Heron QC."
Carter's resignation takes effect immediately.