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Nation put on a masterly display of riding to rack up seven wins from seven stages in the race.
The event was centred around the three peaks of Flagstaff, Mt Cargill and Signal Hill.
Riders were timed on the descents but still had to ride between the stages, which is part of the enduro format.
Christchurch rider Renee Wilson won the women's grade.
Nation, the defending champion, finished more than a minute clear of former Dunedin rider Justin Leov, now of Blenheim.
Dunedin rider Ethan Glover was third.
Nation said he didn't expect to be so close to Leov, let alone beat him.
``I am feeling fit and my training and my bike is going so well at the moment. I suppose if ever there was a time that I could run close to him [Leov] then this would be it,'' he said.
Nation said he was positive he could ride the greasy conditions on Signal Hill on the second day.
``We had similar conditions last year, so I was pretty confident I could ride the greasy conditions up there and I managed to slide my way down the hill three times and do all right.''
Leov, who has been recovering from glandular fever that struck him down earlier this year, said settling for second place was acceptable.
``I felt better and better through the day, but before the last stage I knew I had used most of my energy. I'm not quite in the condition I need to be, but at this time of year I am happy with where I am at,'' Leov said.
Leov tied with Nation on the second stage, but could not match or better him on any other.
``I'm friends with Joe and I am stoked for him and to see him on such good form here. I was hoping I could reel him in a bit on Signal Hill, but he was just in another league.''
In the women's race, Wilson was in an arm-wrestle with Amanda Pearce, of Nelson, for the lead all weekend.
A costly mistake for Pearce in stage five eased the pressure on Wilson, but Pearce was not about to give up, taking wins in the final two stages.
In the end it was not enough to close the gap, with Wilson taking the title by a 39sec margin after seven stages. Melanie Blomfield, of Christchurch, was never far off the pace, finishing third, while Melissa Newell, of Wanaka, slotted into fourth ahead of Agata Bulska, of Poland.