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Dr Clark was nabbed after parking his signwritten van at the car park - 2.3km or roughly five minutes drive from his Opoho, Dunedin home - and it was spotted by someone who dobbed him in to media.
A Toyota Hiace van, emblazoned with Clark's face, was snapped parked near Signal Hill Lookout earlier on Thursday.
A concerned member of the public sent photos of his van parked in the Logan Park High School car park to Stuff saying they were "horrified" and questioned whether Ministers and their families were above the law.
On social media it has prompted similar reactions from some readers, while others have said the mountain bike track was not far from his home and questioned whether Dr Clark did anything wrong.
Dr Clark confirmed his trip, saying he went for a bike ride between video conference meetings. "As Health Minister I try to model healthy behaviour and this afternoon I decided to fit in a bike ride between video-conference meetings. "This was my only chance to get out for some exercise in daylight hours," he said.
However, his boss Prime Minister Jacinda Ardern has repeatedly advised locked down Kiwis to stay local - and if they want to exercise to do so near their home.
The message has also been hammered home by Police Commissioner Mike Bush, who has said that vehicles should only be used for grocery shopping or a medical trip.
The 6km mountain bike trail, dubbed "The Big Easy" was not challenging and was a popular local destination, Dr Clark said.
"I know that now is not the time for people to be engaging in higher-risk exercise activities," he said.
Dr Clark said the bike track was "not challenging"
NZ Herald and ODT