In 2001 he guided the New Zealand Colts side for a season and in 2002 was the assistant coach at the Crusaders. Following the dismissal of Graham Mourie as Hurricanes coach Cooper was appointed to take over the franchise and came to prominence by guiding them to the semi-finals in two of his three seasons in charge.
Cooper led the New Zealand Colts for a year in 2001 and worked as an assistant coach at the Crusaders in 2002. Following Graham Mourie's dismissal, Cooper became head coach of the Hurricanes and gained prominence by leading them to the semi-finals in two of his three seasons.