Speaking at a conference in Tokyo, Motegi said the measures had been taken "based on facts" over concerns of the rapid spread of the coronavirus.
South Korea has expressed "extreme regret" at the move and warned of retaliation if Tokyo doesn't withdraw the restrictions.
Motegi said: "This step is not something we used as a diplomatic measure. This is introduced in order to respond to and prevent a further expansion of coronavirus in Japan, as we are at a critical juncture for the spreading of the virus."
He added the measure will last until the end of this month.
South Korea has confirmed more than 6,500 cases of the coronavirus, but its numbers of new cases have been declining in recent days.
Meanwhile China has reported 80,552 cases, more than 80% of the world's total.
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