The Department of Conservation is investigating the shooting of two South Island pied oystercatchers found dead near the upper Manuherikia River during Labour Weekend holiday.
Although not endangered, the birds are protected native wildlife.
If they had been deliberately killed, which is an offence under the Wildlife Act, people can be fined up to $100,000 or jailed.
"This kind of behaviour is really appalling," Doc Central Otago community relations manager Jacob Dexter said.
The birds were most likely a breeding pair as they were found in a typical nesting area of a stony riverbed, he said.
Bullets were found inside the birds when they were dissected.
The South Island pied oystercatcher is found throughout New Zealand but only breeds in the South Island on riverbeds, lake fringes, and sub-alpine areas in low vegetation.
Breeding mainly occurs from September to November.
If threatened the birds can become aggressive during the season.
