Cowie has also officiated more than 100 first-class games in an umpiring career which spanned 20 years, and was one of three New Zealand representatives on the International Cricket Council (ICC) international panel.
The Kiwis are currently represented by Billie Bowden on the elite panel, while Tony Hill and Evan Watkin are the remaining representatives on the international panel.
All Test playing countries have three representatives on the panel, but for now it is unclear who will replace Cowie.
"I am still dedicated to the game and passionate about improving the role of modern umpires in cricket," Cowie was quoted as saying in a media release.
"However, the satisfaction gained from the challenges of umpiring no longer outweigh the sacrifices necessary to perform on the field. Recent changes to cricket and umpiring have placed greater demands on umpires and I feel the time is right to refocus my priorities," he added.