The environmental affairs department has approved an annual quota of 1 500 lion skeletons for export, it announced on Monday.
Spokesperson Albi Modise said the quota, which was effective from June 7, was based on new evidence from a research project on the lion bone trade in South Africa.
The project was established by the SA National Biodiversity Institute (Sanbi) in collaboration with the University of the Witwatersrand, Oxford University and the University of Kent.
He said the study revealed, among other things, that there had been no discernible increase in the poaching of wild lions in the country, although there appeared to be an increase in the poaching of captive bred lions for body parts.
The study showed that there appeared to be a growing stockpile of lion bones in the country.
"If there is ongoing demand for lion bone and the supply from captive breeding facilities is restricted, dealers may seek alternative sources, either through illegal access to stockpiles or by poaching both captive bred and wild lion," he said.
"South Africa has learned through its experience with rhino and abalone poaching that these illegal supply chains are very difficult to disband once they become established and seeks to avoid such a scenario materialising."
The determination was communicated to the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) Secretariat.
The department said that around 7 000 lions were in around 260 captive breeding facilities.
"Hunting is part of South Africa's policy of sustainable utilisation of natural resources - a principle supported by multilateral environmental agreements such as CITES and the Convention on Biological Diversity (CBD)," said Environmental Affairs Minister Edna Molewa.
"All activities involving the African lion, including hunting, possession and trade are regulated through a permit system; and our policies are supported by solid scientific evidence."
Any application to export lion bones has to be lodged with provincial conservation authorities, who then confirm the availability of a quota.
If a permit is then issued, it has to indicate the permitted quota.
All skeletons had to be packed separately at the source, after they were weighed, tagged and DNA samples were taken.
The consignments have to be inspected and weighed at exit ports to confirm the information on the permit.
A number of non-governmental organisations (NGOs) and conservationists opposed to the trade in lion bones previously voiced their disapproval to News24.
Dr Paul Funston, senior director of wild cat conservation group Pantheras Lion Program, warned at the time that the legislation of a trade in lion bones would stimulate the market and endanger both captive and wild lion populations.
"There is significant evidence that South Africa's legal trade in captive-bred lion trophies is accelerating the slaughter of wild lions for their parts in neighbouring countries and is, in fact, increasing demand for wild lion parts in Asia - a market that did not exist before South Africa started exporting lion bones in 2007."