The high performance manager of Swimming New Zealand, Jan Cameron, has announced she is resigning.
She is to leave the job at the end of the week.
Ms Cameron said it was not in the best interests of the sport for her to remain in her position.
In June, an independent review of top-tier swimming commissioned by Sport and Recreation New Zealand (SPARC ) was highly critical of the sport's high-performance programme and singled out Ms Cameron as a problem.
She says she doesn't agree with many of the report's findings but ongoing debate about the state of the high performance programme is not in the best interest of the sport.
She cites the recent 12 medals won at the University Games in China and the performances at the World Champs in Shanghai, where seven national records were set, as something the country can be proud of.
Critic welcomes Cameron resignation
The chair of Swimming New Zealand, Murray Coulter, resigned on Friday 2 September.
The swimmer who triggered the review, Moss Burmeister, has welcomed Ms Cameron's resignation, saying there needs to be an overhaul of what is a "restrictive" high-performance programme.
Mr Burmeister says the Swimmers' Association, of which he is a board member - has drawn up a blueprint for a high-performance programme which they have given to Swimming New Zealand and SPARC.
He retired after the 2010 Delhi Commonwealth Games saying there was a lot of distrust in the high-performance programme and that swimmers were too scared to voice their concerns for fear of being dropped from the national squad.