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The sheep were discovered "packed in like sardines" in the Mitsubishi L300 van after police tracked the vehicle to a property after being spotted being driven erratically in the city around 2am.
Senior Sergeant Maui Aben said the sheep seemed in good health and did not appear distressed.
They were handed over to the Gisborne District Council's animal control unit.
It was not known where the sheep were stolen from, but police were researching ear tag information on the sheep.
"Rustling is a major problem for rural areas not just in the Tairawhiti area, but all across the country. It impacts heavily on our local communities and stock losses place a heavy financial burden on our farmers. This activity will not be tolerated and police will be coming down hard on anyone who steals stock," Mr Aben said.
Two youths, aged 16 and 17, will appear in the Gisborne Youth Court today.