"We've had more people wanting to be circumcised than our resources can actually manage. In fact, we're overwhelmed," South Africa's KwaZulu-Natal province Health Minister Sibongiseni Dhlomo told the BBC.
Some studies suggest circumcision can help men halve their chance of contracting the human immunodeficiency virus, which causes AIDS, and a prisoner's advocacy group supports the procedure.
South Africa's Prisoners Human Rights Organization told the BBC it welcomed the move as long as inmates were properly informed.
"It may help fight the scourge of HIV/AIDS, which appears to be spreading like wildfire in South African prisons," said Golden Miles Bhudu, a spokesman for the PHRO.
More than 10,000 men have been circumcised since the program started in April, Dhlomo said.
In South Africa, about 5.7 million people are infected with HIV, and there are about 1.4 million AIDS orphans. About 350,000 Africans died of AIDS in 2007, the report said.