News agency Reuters on Sunday reported that at least six soldiers were killed in clashes with the rebels according to a witness.
"I saw the bodies of six South African soldiers. They had all been shot. Their vehicles were also destroyed. Other South African soldiers came to recover the bodies," the witness told Reuters.
However the South African National Defence Force (SANDF) could not confirm the deaths.
"We are working on a statement," Brig-Gen Xolani Mabanga said.
He said the SANDF was currently assessing and verifying information and once that was complete a statement would be issued.
Mabanga said the SANDF's position would be based on the outcome of the assessment.
He could also not disclose the number of South African soldiers in the CAR for security reasons.
More SA troops sent
Earlier the SANDF issued a statement saying it had deployed more troops to the CAR following days of clashes between armed forces and rebels.
"Following changes in security situation in the CAR the SANDF sent in some more support to protect its personnel and equipment," Mabanga said.
He said the SANDF has been deploying troops to the CAR since 2007 following a memorandum of understanding between the two countries. However since the recent changes in security situation more troops had been sent.
"Since then the security situation deteriorated."
Mabanga said an SANDF base on the outskirts of Bangui, the CAR capital, came under attack on Saturday. SANDF troops managed to drive back the rebel forces.
CAR president flees
"The chief of the SANDF has emphasised that the SANDF reserves the right, at all times, to act decisively in defence of its members and assets deployed on the ground in CAR."
CAR President Francois Bozize fled the capital early on Sunday after hundreds of armed rebels threatening to overthrow him invaded the city, the Associated Press reported.
And by Sunday afternoon the rebels reportedly took control of Bangui.
The rebel alliance, known as Seleka, reached the outskirts of Bangui late on Saturday and the fighters seized the presidential palace on Sunday.
Rebels from several armed groups that have long opposed Bozize joined forces in December and began seizing towns across the country's sparsely populated north. They threatened at the time to march on Bangui, but ultimately halted their advance and agreed to go to peace negotiations in Libreville, the capital of Gabon.
A peace deal was signed on January 11 which allowed Bozize to finish his term that expires in 2016, but the rebels soon began accusing the president of failing to fulfil the promises that were made, the Associated Press reported.
They demanded that Bozize send home South African forces that were helping bolster the country's military. And they sought to integrate some 2 000 rebel fighters into Central African Republic's armed forces.
The deal unravelled more than a week ago, with the rebels again taking control of two towns and threatening to advance on the capital. – Sapa