KakaoTalk is operated by South Korea's Kakao Corp., while Line is run by a Japanese subsidiary of South Korea's biggest portal Naver.
The ministry said it had been informed by Beijing that there was evidence terrorist groups were using messaging apps to "plot and incite" attacks.
"The ministry will continue negotiations with Chinese authorities so that users' inconveniences be resolved at the earliest possible date," the director of its Internet Policy unit, Lee Jin-Gyu, told reporters.
Lee said other foreign messaging services like Didi, TalkBox and Vower had also been affected.
China blocks access to a host of websites including YouTube and Twitter using a system known as the "Great Firewall", and restrictions are tightened before dates the government considers sensitive.
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