The World Anti-Doping Agency (WADA) has suspended the South African Doping Control Laboratory in Bloemfontein until September 30.
The suspension comes into force immediately and prevents the facility from carrying out all anti-doping activity, including the analysis of blood and urine samples.
During the period of the ban, samples will instead have to be taken to another WADA-accredited laboratory.
According to Associated Press, athletics powerhouses Kenya and Ethiopia are among the countries to send samples to Bloemfontein.
No clear reasons for the suspension have yet been revealed, but the laboratory will have failed guidelines set-out by the International Standard for Laboratories (ISL).
WADA said the laboratory would need to "address all non-conformities identified in its External Quality Assessment Scheme (EQAS) programme and any other non-conformities identified in the course of WADA site visits during the suspension period".
If the laboratory satisfies the Disciplinary Committee in meeting these requirements, it may apply for reinstatement prior to September 30.
WADA will be making site visits to South Africa and its decision can be appealed at the Court of Arbitration for Sport.
Last month, WADA revoked the accreditation of the Moscow Laboratory in Russia.
They had initially suspended the facility on November 10, following the WADA Independent Commission reports which revealed evidence of widespread state sponsored doping in Russian athletics.
Cover-ups and the destruction of samples were also revealed, and suspending the laboratory, which is at the centre of the scandal, was a key recommendation.
Its accreditation has now been completely revoked, with WADA saying the laboratory accepted this verdict.
WADA is responsible for monitoring laboratories to make sure they are in line with the ISL.
The organisation also suspended the accreditation of the Laboratório de Análises de Dopagem in Lisbon, Portugal, in April after this too failed to meet the ISL requirements.
A further decision regarding possible revocation of the laboratory’s accreditation will be made by WADA’s Executive Committee.