Of those discovered, more than 400 have died, a veterinarian at the Johannesburg zoo said. The remainder of the creatures were taken there for treatment and most have stabilized.
It's believed the animals were without food or water for five days, the BBC reported Saturday.
"A substantial number have stabilized, eating and drinking, there are about over 1,200 that have survived -- others with irreparable damage," the zoo's veterinarian Brett Gardener said.
They were headed to the United States for sale as exotic pets. Most of the creatures were stuffed in muslin bags or small plastic containers.
The problem came when the flight the animals were scheduled to board was delayed indefinitely due to inclement weather, stranding them in a cargo holder for days, the BBC said. Inspectors found the animals Wednesday after workers reported a "bad smell" coming from the containers.
Animal rights groups are investigating the incident and said they plan to bring animal cruelty charges against those responsible for the poor conditions the animals were left in.