The samples will be sent to the National Control Laboratory for quality assurance.
More than 325,000 doses of Pfizer’s Covid-19 vaccine arrived at OR Tambo International Airport on 2 May.
Health minister Zweli Mkhize said a National Joint Operational and Intelligence Structure (NATJOINTS) was on guard to monitor the security of the transportation of the vaccine at the airport and to ensure the safe passage of the vaccine to various vaccination sites.
The samples will be sent to the National Control Laboratory for quality assurance and, after release, will be distributed to the provinces, said Mkhize.
The health ministry expects to receive 1.3 million doses from Pfizer by the end of May, which will be delivered in weekly batches of approximately 325,000 a piece.
South Africa will have received 4.5 million vaccines by the end of June.