"We receive ongoing complaints like that from a lot of the informal areas, but in Alexandra the owls are being supplied for that," said Owl Rescue director Brendan Murray.
"They kill the birds, they decapitate them, they take their eyes out. Last week, we had a case where school kids caught an owl and cut its legs off with a pair of scissors."
A case of animal cruelty had been opened with the National Council of the Society for the Prevention of Cruelty to Animals (NSPCA).
Murray said it was trying to stop the city from releasing more owls in Alexandra.
"We have spoken to the town council about this. We are saying rather use the R2.5 million to employ people to catch the rats.
"You can employ 100 people to catch them with traps, just find another way. The owls are not viable at all."
In September, the City of Johannesburg said it included barn owls in a R2.5m plan to fight the rat infestation.
Mayoral committee member for health Nonceba Molwele said owl boxes had been placed at four schools in Alexandra, each containing four owls.
Another owl box was placed at the Marlboro Gardens Combined school.
Barn owls are the rodents' natural predators.
Last month, Jonathan Haw from Eco Solutions said one owl could feed on many rats in a month. Over 83,000 owls had been released in various parts of Gauteng since 1998.
Source : Sapa