Waddell, who won gold in the single sculls at the Sydney Olympics, replaces the now retired Dave Currie, who attracted criticism at the London Olympics over his team management.
"It's a unique position and I'm honoured to have been appointed," the 37-year-old said.
"I've been to three Olympic Games and experienced them not just as a successful gold medal winner but also as a wide-eyed first-timer and again as an athlete struggling to meet expectations.
"That broad perspective will help better understand our top athletes."
Currie drew criticism after several competitors, including shot-put champion Valerie Adams, were not officially entered in their respective events in London, while his penchant for doing the haka in the stands and at the athletes' villages at Olympics and Commonwealth Games also raised eyebrows.
Waddell, who overcame a heart condition that caused an irregular heartbeat to win gold in Sydney, has been involved with New Zealand's America's Cup challenge since 2001.
He made a return to rowing in 2008, combining with Nathan Cohen to finish fourth in the double sculls at the Beijing Olympics, before he returned to the America's Cup setup.
His new role will not conflict with New Zealand's America's Cup campaign next year.
"Rob has what it takes to make sure the environment is right for athletes to achieve at Olympic Games," NZOC Secretary General Kereyn Smith said.
"He knows sport and the needs of elite athletes, is highly respected and sets a clear standard of excellence."
- Sports & Recreation
- Sydney Olympics