Both defended their national titles, following up from their victories at the recent Oceania Championships in Dunedin.
The cross-country competition was moved to Hawea Flat after snowfall made the initial course at Cardrona unsuitable.
Cooper, the world No7, won by nearly 3min after breaking away early on.
"I got a wee gap at the start and from there I had a steady pace.
"I focused on not making any mistakes and to get to the line in one piece," he said.
Sheppard said the day was "fantastic" and the course was unique.
"It was a different type of track today — quite punchy and the hills were a lot shorter.
"I enjoyed the challenge. It was different to what we have had all season and it went perfectly to plan."
Both riders head to South Africa this week to prepare for the opening round of the UCI World Cup before they return home to prepare for April’s Games.
There were a couple of surprise upsets in the downhill competition at Cardrona yesterday.
New Plymouth’s Ed Masters claimed the elite male competition, while Oceania champion Sam Blenkinsop and defending champion Keegan Wright failed to make the podium.
Likewise, heavily favoured Shania Rawson, an under-19 world silver medallist, lost out to Aucklander Kate Weatherley.
Full results can be found on Cycling New Zealand’s website.
