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Senior Sergeant Mark Crawford, of Dunedin, said police were called to the crash, involving a Honda CRF 400cc dirt bike, at the corner of Argyle St and Elgin Rd about 1.30am.
The serious crash unit was investigating, he said.
A St John spokesman said the man was taken to Dunedin Hospital at 2.24am.
A Fire Service spokesman said a St Kilda Station crew washed down the road.