cotter later worked as a rowing coach. this included coaching the men's coxed four who won silver at the 1988 seoul olympics. in december 2008, he succeeded andrew matheson as high performance director for rowing new zealand; matheson had not returned to new zealand from the 2008 summer olympics after receiving an offer from rowing australia. he faced funding pressure from high performance sport new zealand after missing the target of five rowing medals at the 2016 rio olympics, where only three medals were won. he resigned from rowing new zealand in august 2018 over allegations of bullying.