Bird Rescue Dunedin, in St Kilda, is a non-profit charitable organisation that rehomes birds.
Founder Sue Cook said she cared for at least 400 birds each year, including mallards, blackbirds, magpies, pukeko, seagulls and even roosters.
"I don’t know what to do. They’ve left me nothing except telling me that I’ve got six months."
All her neighbours knew about the aviaries and had been happy with them.
They were regularly checked by the Department of Conservation (Doc) and visited by the Dunedin City Council (DCC).
On Monday, she was told by a council staff member she had six months to dismantle her aviaries and needed to get consent to rebuild them under new specifications.
She had not yet received any formal letter from the council and did not know the nature of the complaint against her.
"I was aware there was a lot of aviaries right on the fence line, but my neighbours were all happy and everyone knew about them, including the DCC.
"It wasn’t an issue unless someone complained."
The organisation received no grant funding and was run on donations from the community.
Rebuilding was not an option as the cost was too great.
Hers was the only rescue operation in Otago that took in all types of birds, and the only one in Dunedin open in the evenings.
It would be a "huge loss" to the community if the aviaries were dismantled, she said.
He confirmed staff visited the site on Monday, but said no notices had been issued at this point.
Doc Coastal Otago supervisor Jim Watts said Bird Rescue Dunedin held a Wildlife Act Authority from Doc to rehabilitate sick or injured birds.
Doc did not regularly take sick or injured birds to them.
- Additional reporting Matthew Littlewood