DeepSeek's R1 chatbot stunned investors and industry insiders with its ability to match the functions of its Western competitors at a fraction of the cost.
But a number of countries have questioned DeepSeek's storage of user data, which the firm says is collected in "secure servers located in the People's Republic of China".
Seoul's Personal Information Protection Commission said DeepSeek would no longer be available for download until a review of its personal data collection practices was carried out.
The Chinese AI firm has "acknowledged that considerations for domestic privacy laws were somewhat lacking", the data protection agency said.
It assessed that bringing the app into line with local privacy laws "would inevitably take a significant amount of time", the agency added.
"To prevent further concerns from spreading, the commission recommended that DeepSeek temporarily suspend its service while making the necessary improvements," it said.
DeepSeek has "accepted" that proposal, it added.
- 'Use with caution' -
The app was removed from local app stores on Saturday at 6:00 pm (0900 GMT) and remains unavailable.
The AI chatbot is still in use for those who have already downloaded the app.
Seoul's data protection agency said it "strongly advised" people to "use the service with caution until the final results are announced".
That included "refraining from entering personal information into the DeepSeek input field", it said.
Analyst Youm Heung-youl told AFP that the firm was yet to lay out a privacy policy "specifically tailored" for users in South Korea.
"It has on the other hand disclosed a privacy policy for the EU and certain other countries, stating that it complies with the domestic laws of those nations," Youm, a data security professor at Soonchunhyang University, said.
"Deepseek needs to establish a privacy policy specific to Korea," he said.
Asked about the app's removal, Beijing said on Monday that it asked Chinese firms to operate on "overseas operations on the basis of strict abidance by local laws and regulations".
Chinese foreign ministry spokesman Guo Jiakun also urged "relevant countries" to "avoid taking measures that overstretch the concept of security or politicise trade and technology issues".
This month, a slew of South Korean government ministries and police said they blocked access to DeepSeek on their computers.
Italy has also launched an investigation into DeepSeek's R1 model and blocked it from processing Italian users' data.
Australia has banned DeepSeek from all government devices on the advice of security agencies.
US lawmakers have also proposed a bill to ban DeepSeek from being used on government devices over concerns about user data security.
In response to the bans, the Chinese government has insisted it "has never and will never require enterprises or individuals to illegally collect or store data".
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