The National Council of Societies for the Prevention of Cruelty to Animals (NSPCA) found that more than 6 000 sheep had contracted a virus at an Eastern Cape feedlot and could not board the Al Messilah "death ship".
On Tuesday, the ship docked at the East London harbour, where more than 50 000 sheep and thousands of cattle were set to be loaded onto it.
However, the NSPCA said it was greatly concerned about the conditions of the animals.