The dwindling rook population has resurfaced in Maniototo and about 20 rooks have been spotted on a Kyeburn farm.
The Otago Regional Council is now "keeping an open mind" about rook numbers which were previously thought to have been declining.
The population was believed to have been fewer than 40 less than a year ago, down from thousands in the 1990s.
Council biosecurity and biodiversity team leader Richard Lord said staff had responded to a reported sighting this week and staff were now surveying known rook sites in the area.
"Fog hindered some recent site inspections, but we'll continue the search and will implement appropriate control measures if any are located."
Rooks are included in council's proposed regional pest plan as a pest to be eradicated.
The council said large flocks of the birds could inflict thousands of dollars' worth of damage to Otago's grain and new grass crops.
Rooks had previously been spotted in the Patearoa and Gimmerburn areas of Maniototo.
Lord said the council could not say whether the population might have grown until more information had been gathered.
"We are keeping an open mind.
"This is why it is so important that people stay vigilant and report rook sightings to ORC."
The council's pest plan prohibits unauthorised individuals from poisoning, capturing, trapping or shooting at rooks, or interfering with a rook nest as it could result in the rook population scattering and new colonies being formed.
"The small population of rooks in the region make it difficult to identify and destroy them, meaning reports from the community are essential," Lord said.
• If you have rooks on your property or observe them anywhere in Otago, please report them to the Otago Regional Council by calling 0800 474 082.