Matheson said working in Australia with the rowing programme has been a fantastic experience, but he didn't have to think twice about returning home.
"I've got a lot of respect for the people I've worked with in Australia and the progress we've made. But when the opportunity came along to return to my home country, to play a significant part in an organisation that's already making headway in high performance sport, I leapt at it."
High Performance Sport New Zealand chief executive Alex Baymann said he was thrilled to attract someone of Matheson's calibre back home.
"New Zealanders working in high performance sport are often highly sought after," he said. "We've lost some of our best coaches and high performance directors to jobs overseas over the years.
"Andrew will drive our investment approach to ensure we produce more Kiwi winners, and he'll work strategically with national sport organisations to develop world-leading high performance programmes, which enable our athletes and coaches to perform at their best."