Hundreds of Confucius Institutes around the world promote Chinese traditional culture and language as part of Beijing's soft power strategy. They have provoked controversy over issues of academic freedom at some Western universities.
The state-run network has dozens of branches in South Korea in partnership with local colleges.
But Seoul and Beijing are in an increasingly heated dispute over a plan to deploy the powerful US anti-missile system THAAD to the South against threats from nuclear-armed North Korea.
Now Seoul's immigration authorities have since December stopped issuing new visas or extending existing ones for Chinese teachers, Yonhap news agency said.
There are 22 Confucius Institutes in South Korea, the third-highest of any country following the United States and Britain, it said.
An official at Andong National University in the southern city of Andong -- which hosts a Confucius Institute with seven Chinese instructors -- confirmed the report.
The teachers have been formally employed and paid by the Chinese government, in violation of rules that require visa holders to be hired and paid by South Korean employers, said the official.
"The practice has somehow been tolerated for years... until recently," said the official, adding it is the first time that Seoul has taken issue with it.
"Something like this never happened before," she said.
The justice ministry was not immediately available for comment. An unnamed ministry official told Yonhap that there was "no motive" behind the latest move.
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