Molnupiravir and a rival antiviral pill from Pfizer called Paxlovid have demonstrated efficacy in trials of adults with Covid-19 who are at high risk of serious illness and are now both in use.
Countries around the world are negotiating prices with Merck and Pfizer. The US government is paying $700 for each course of molnupiravir, but generic drugmakers will make less expensive versions in a deal aimed at giving access to poorer nations.
Regulator SAHPRA said in a statement that molnupiravir was indicated for use in patients aged 18 years and older. It authorised, with conditions, the importation of a limited quantity of molnupiravir capsules for six months at first.
"The authorisation of molnupiravir for compassionate use offers further therapy in the fight against Covid-19," Boitumelo Semete-Makokotlela, chief executive of SAHPRA, said.
But health department Deputy Director-General Nicholas Crisp said that an evaluation score from the National Essential Medicines List Committee indicated that Merck's pill would not be cost effective.
"We are not planning to procure molnupiravir," Crisp said, adding that the advisory committee was yet to evaluate Pfizer's Paxlovid. However, the private sector can buy whatever is allowed by SAHPRA since medicines are not like vaccines which are sold to governments only, he added.
SAHPRA said on Thursday that Pfizer had applied for authorisation of use of Paxlovid and it was considering the application.
South Africa has recorded more Covid-19 cases and deaths than any other country in Africa, after four infection waves. In late November, it alerted the world to the highly transmissible Omicron coronavirus variant.