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The three lambs were being kept in a paddock next to his home in Cemetery Rd, beside the East Taieri Church, with about 15 other lambs and ewes.
A ewe was also shot in the head but at this stage was still alive, Mr Nimmo said.
It appeared a .22 rifle had been used, he said.
''You don't expect it because it's right beside the church and only a stone's throw from my house, and [for] somebody to be shooting a gun that close to my house is almost as big of a concern as the killing of the lambs.''
Police had been called and two officers visited the paddock late yesterday afternoon, he said.
A police spokesman said an investigation into the shooting was ongoing.