"We ask our athletes to do extraordinary things and we're enormously proud of them when they achieve," he said.
"That's one of the reasons we invest in high performance systems through the nation.
"We have a duty of care to make sure we have that balance between winning and ensuring it's a safe environment that respects them and allows them to grow as people. Maybe that balance has not been right."
Miskimmin said Sport NZ's investigation was commissioned independently before the cycling and football controversies came to light. The concurrent inquiry into High Performance Sport New Zealand's actions is ongoing.
Miskimmin said working with athletes through their respective players associations was pivotal to the success of any arrangement.
"Look at the All Blacks and Black Caps environments where the focus has been on creating good people and providing them with a voice through their players' associations.
"The football situation is another example. Athletes had concerns which they raised with the players association, who raised it with executives and now it's being dealt with as an employment issue.
"That is a good mechanism but it's not the case in every sport, especially Olympic and Paralympic sport."
Miskimmin said philosophies had changed worldwide.
"Our colleagues in the USA and UK are all looking at the best ways to create the right performance environment.
"For a long time in sport we've had a command and control culture, that's not fit for purpose today.
"What athletes are saying is that we ought to be involved and want to have confidence to raise issues, and we want to be at the table when decisions are made around us and about us."
New Zealand Athletes' Federation general manager Roger Mortimer shared his concerns with the Herald earlier this month in the wake of the cycling allegations.
Mortimer comes from a background managing Olympic gold medallists Sarah Ulmer, Hamish Carter and Mahe Drysdale.
"What has become increasingly worrying over the last decade has been the increased anxiety levels amongst coaches and athletes associated with the need to produce medals at almost all costs," he said.
"Everyone involved in sport at that level wants to win. The problem is when this overrides areas such as respect for culture, people and environments.
"Sport is a privilege for anyone isn't it? The lean away from people towards outcomes at almost any costs has become a real worry in so many areas."