"Whenever difficulties and challenges arise in South Korea-China relations... We should not over-react," Yun Byung-Se said in a briefing to local reporters.
The dispute has its roots in the announcement last month that South Korea would deploy a sophisticated US anti-missile system to counter the growing threat from North Korea's nuclear weapons programme.
China condemned the deployment of the Terminal High Altitude Area Defense (THAAD) system as a move against its own national security interests and a threat to regional stability.
In any conflict between China and the United States, "South Korea will inevitably be the first target," the newspaper said.
China is South Korea's largest trading partner and accounts for one quarter of its exports.
It is also a key market for popular South Korean entertainment exports like K-pop and K-dramas, which seem to be the initial targets of a gathering anti-THAAD backlash in China.
A "fan-meeting" scheduled for this weekend in Beijing with the stars of a popular Korean drama series was abruptly cancelled on Wednesday.
An appearance by the Korean boy-band Snuper on a Chinese TV music show was also cancelled at the last minute.
"The show itself will go on and it's just Snuper who won't be performing," said a spokeswoman for the band's agency, Widmay Entertainment.
"We are trying to determine the reason," she added.
Foreign Minister Yun said the government in Seoul was keeping a "close watch" on the Chinese media reaction to THAAD and what he described as "other measures" being taken in China.
THAAD has also been the subject of domestic protests, particularly by those living in the rural county of Seongju where the first battery will be installed.
Residents say the system's powerful radar poses health and environmental hazards and argue that its presence will make them a key military target.
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