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Acting Central Otago sub-area supervisor Detective Sergeant Derek Shaw said the man, thought to be from Dunedin, was clearing manure from under the floor of the woolshed on Glenbrae Station.
The man's workmate, who investigated when he noticed the digger had not moved for a while, found his co-worker trapped, Det Shaw said.
Det Sgt Shaw said the injured man had sustained serious head and chest injuries and was listed as still in a critical condition in hospital last night.
Victim Support had been talking to the co-worker.