China considers self-ruled Taiwan as part of its territory and has sought to whittle down the number of countries that recognise its claim to statehood.
"We have been asked to move our representative office out of the capital (Pretoria)," an official from Taiwan's foreign ministry told AFP on condition of anonymity.
"Our reasonable conclusion is that it is part of a series of actions by China to suppress Taiwan," the official said.
"We are still negotiating with South Africa in the hope that there will be room for change."
The official did not say when Pretoria issued the order or when the deadline was for Taiwan to move its office.
South Africa's foreign ministry defended the decision in a statement, saying it had been "mischaracterised" and was only meant to reflect Pretoria and Taipei's "non-political and non-diplomatic" relationship.
The Taipei Liaison Office (TLO), which is set to be rebranded as a trade office, "will be appropriately placed in Johannesburg, South Africa's economic hub," said Chrispin Phiri, South Africa's foreign ministry spokesman.
"This also aligns with standard diplomatic practice that capital cities are the seats of Foreign Embassies and High Commissions," he said.
According to the foreign ministry, the South African Liaison Office (SALO) in Taipei will also rebrand as a trade office.
Taiwan's semi-official Central News Agency said Thursday that South Africa issued the order on October 7 and gave the representative office until the end of the month to move.
According to Pretoria, Taipei was given six months.
China said Friday that South Africa had made the "right decision".
"Taiwanese independence advocates do not enjoy popular support and are doomed to failure," Chinese foreign ministry spokeswoman Mao Ning said.
Taiwan has 12 diplomatic allies, with most nations, including South Africa, instead recognising Beijing.
In 2017, Nigeria ordered Taiwan to shut down its trade office in the capital Abuja in what Taipei said was an attempt by Beijing to push it out of the country.
Relations between Beijing and Taipei have been fraught for years and have spiked since Taiwan President Lai Ching-te took office in May.
Lai is more outspoken than his predecessor in defending Taiwan's sovereignty, with Beijing calling him a "separatist".
On Monday, China deployed fighter jets, drones and warships to encircle Taiwan in the fourth round of large-scale military drills in just over two years.
Taipei condemned Beijing's actions as "irrational and provocative", and the island's key backer and biggest arms supplier Washington called them "disproportionate".
Beijing said the drills were a "stern warning to the separatist acts of 'Taiwan Independence' forces".
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