Rowing New Zealand high performance manager Alan Cotter has delivered a shock resignation after overseeing a record decade-long run of medals in the sport, including the anointment of five Olympic champions.

His decision follows an internal review midway through the Olympic cycle, to provide what the governing body described as "insights free from the emotions that can surround 'pinnacle' events".

A source told the Herald the review dealt with rowing's culture and whether the desire for medals was trumping athlete well-being.

A similar exercise took place after the Rio Olympics.

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Surprisingly, neither Cotter nor chief executive Simon Peterson were prepared to comment on his legacy.

Sources told the Herald both rowing reviews addressed a culture of fear and a lack of transparency in the sport which extended back years.

A Rowing NZ statement said "no formal complaints or allegations" had been made about Cotter or the governing body.

"The well-being of our athletes and the culture of our organisation is paramount to everything we do," it read.

"We are constantly evaluating how we are performing.

"It is important we are not looking backwards at the outcomes of campaigns but continue to look forward, so we can refresh and continually improve to maintain our place as world leading in the high performance environment.

"Alan Cotter agreed to resign for this to occur."

Rowing NZ will receive $5.1 million in taxpayer funding this year to maintain its high performance programme but, in a blow to accountability, said the review will remain confidential out of respect to those who participated.

Cotter will depart after the September 9-16 world championships in Bulgaria.

He joined the organisation in 2008, replacing incumbent Cycling New Zealand chief executive Andrew Matheson after the Beijing Games.

The 61-year-old's pedigree included bronze and silver medals as coxswain of the New Zealand eight at the 1978 and 1979 world championships.

Eric Murray:
Eric Murray: "I was told that I should be thinking about my career, not about having children." Photo / Photosport

New Zealand consistently achieved in the upper echelons of medal tables during his tenure.

New Zealand Athletes' Federation boss Roger Mortimer could not comment specifically about the Cotter situation, but said it was vital athletes had a voice in high performance programmes.

"In the 1980s we had strong, vocal athletes like Dame Susan Devoy, Erin Baker, Rick Wells and various rugby players and cricketers.

"I think athletes now have a fear about expressing their opinions. It provides a much healthier environment when there is robust debate.

"The greatest misunderstanding in these discussions is that wellbeing and performance are not mutually exclusive."

Several controversies have rocked Rowing NZ's boat in recent years.

In his autobiography, The Kiwi Pair, double Olympic gold medallist Eric Murray wrote he and his wife Jackie were called to a meeting with pair partner Hamish Bond, selector Conrad Robertson, Cotter and coach Dick Tonks to discuss Murray's desire to return home for the birth of his first child prior to the 2011 world championships.

"I was told that I should be thinking about my career, not about having children; Jackie was ostensibly accused of being irresponsible, that the decision to have a child would ruin my career.

"We were talking about one week, and a week in which I would train at home so as to not throw our campaign out of kilter."

Murray wrote that Robertson, the convenor of selectors and a 1984 Olympic coxless four gold medallist, said: "Men didn't come home from war just because women were having children."

"It was the most insane thing I had ever heard, in the worst meeting of my life," Murray said.

Tonks had a falling out with the governing body in 2015 when they questioned him working with a Chinese crew on Lake Karapiro, the same training base of the New Zealand crews.

He was convinced to stay on to coach single sculler Mahe Drysdale and the women's double of Zoe Stevenson and Eve Macfarlane at the Rio Olympics.

Elsewhere, Emma Twigg cut ties with the organisation for the 2015 season because of her decision to train outside the centralised programme.

Twigg had been accepted into the one-year post-graduate FIFA Master course in the management, law and humanities of sport, taught across universities in Leicester, Milan and Neuchatel.

Rowing NZ saw the move as a potential disruption to her Olympic preparation. A compromise could not be reached to allow her to train around study commitments.

At that point she had completed nine years in Rowing NZ's elite programme, culminating in her first world championship gold medal shortly before the decision.