South Africa on Monday said the country had suffered its heaviest military loss since apartheid after 13 soldiers were killed in weekend clashes with rebels seizing power in the Central African Republic.

The troops died in a nine-hour "high-tempo battle", President Jacob Zuma said, as the Seleka rebel coalition advanced on the Central African capital Bangui.

Zuma said 13 soldiers died fighting against "bandits", while one soldier was unaccounted for. The clashes, which erupted on Saturday, also left 27 troops injured.

South Africa deployed 200 soldiers to the country in January following an offensive against the Central African Republic's poorly trained, ill-equipped government troops by the Seleka rebel coalition in early December.

"It is a sad moment for our country," said Zuma.

"Just over 200 of our soldiers fought bandits who wanted to cause harm... but the actions of these bandits would not deter us from our mission of peace and security," he added.

South African National Defence Force spokesman Xolani Mabanga told AFP that it was "the highest number of casualties" suffered since the country's first democratic military was set up in 1994.

The fighting erupted as South African forces sought to defend their military base from rebels closing in on Bangui, according to Zuma.

The rebels' assault has forced deposed president Francois Bozize to flee to neighbouring Cameroon, Yaounde said Monday. Bozize himself seized power in a coup in 2003.

Zuma said the soldiers would remain in the troubled country despite growing calls to bring them home.

"We have not taken a decision to withdraw," Zuma told reporters, citing a pact between the two states.

"Once the dust has settled we will then assess whether our presence there is still needed."

The South African troops were deployed to protect several dozen military trainers who have been stationed in the country for several years.

The defence force's top brass also said the troops would not pull out of the country.

"Our troops are still there until there is a political arrangement. Running away is not an option," military chief Solly Shoke told journalists.

"It was 200 of us against 3,000 rebels," Shoke said, adding that the battles on the outskirts of Bangui against the "well-armed" fighters only ended after the rebels came forward with "a white flag" asking for a ceasefire.

"There is relative truce at the moment," he said, noting that the South African forces were closely monitoring the situation.

"We will do everything within our power to ensure that our troops are protected."

South Africa's National Defence Union national secretary Pikkie Greeff said it was "worrisome" that no decision had been made to bring the soldiers home as the security situation on the ground had changed.

The troops there were not set up for heavy fighting, he said.

"They're well equipped for the purpose that they went there," said Greeff.

"The question is if they are well equipped for conflict? The answer is no, emphatically no."

South Africa and the Central African Republic signed a military cooperation agreement in 2007, which was renewed for another five years in December.

South Africa also has troops in the Democratic Republic of Congo and Sudan.