The move comes as High Performance Sport New Zealand re-examines how the country measures sporting success.
Sources told the Herald the rowing reviews addressed a culture of fear and a lack of transparency in the sport extending back years.
The secrecy was deemed to be at its worst during national trials because athletes were not privy to details of their performances.
The result was that athletes' livelihoods were affected. The effect of not making a team on the basis of data which wasn't readily available could determine whether an athlete earned enough income to remain in the sport.
Cotter was part of the selection panel for crews each year.
Several controversies have rocked Rowing New Zealand'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 rowing 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.
Murray said the selection panel asked Bond privately whether he wanted his crewmate kicked out so he could row with someone else.
"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, looked at him and 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.
"To see my wife demeaned in that way because we'd chosen to have a baby was absolutely appalling."
Tonks had a falling out when he left Rowing New Zealand after his link with a Chinese crew was questioned by the governing body.
Tonks began working with Chinese men's rowers on Lake Karapiro, the same training base of the New Zealand crews, but decided to move on when his link with the rowers was questioned saying they were no threat to top crews here.
When asked whether there had been any fallout, Tonks said: "We're finished. I'm finished with New Zealand rowing."
He was convinced to stay on to coach single sculler Mahe Drysdale and the women's double of Zoe Stevenson and Eve Macfarlane for the Rio Olympics.
Elsewhere, Emma Twigg received no government funding in 2015 because of her decision to train outside the sport's centralised programme at Lake Karapiro.
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 New Zealand saw the move as a potential disruption to her Olympic preparation.
Both parties discussed the matter but compromise was limited. Twigg argued the flexibility of single sculling meant she could train around study commitments. Rowing New Zealand was not convinced, suggesting she defer entry until the year after the Olympics where they would be prepared to offer a sabbatical. Twigg declined that offer.
She had completed nine years in Rowing New Zealand's elite programme, culminating in her first world championship gold medal shortly before the decision.
Yesterday Rowing New Zealand announced its squad for the world championships to be held from September 9-16 in Bulgaria.
