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The potentially deadly virus is considered a biohazard, said South Africa's National Institute for Communicable Diseases (NICD), though the government research centre downplayed the threat of a polio outbreak.
"The risk is fairly small, but we'd like to advise that if the package was found for the public not to tamper with it. Simply return it to the NICD or to the police, " said Adrian Puren, deputy director of NICD.
He said there was no risk the package could be used in a terrorist attack and that the carjackers who stole the courier vehicle carrying it probably did not realise what the box containedâ€“ stool specimens from the Congo being sent to the NICD for polio testing.
The NICD said the vehicle was stolen on Tuesday and later recovered, but that the specimen shipment was missing.
Carjacking is a pervasive problem in South Africa, which has some of the highest crime rates in the world.
Nearly 14, 000 carjackings were reported to police last year.