Chief Cabinet Secretary Yoshihide Suga, however, told a separate press briefing on the matter that Japan will deal with South Korea the same way it treats other countries in the region.
The meeting came two days after Tokyo removed South Korea from its list of nations entitled to preferential trade status.
In July, Japan tightened controls on the export of materials used to make chips, South Korea's top export item, which threatened to disrupt global semiconductor supplies used by tech giants such as Apple and Huawei.
However the moves - which Tokyo has said are based on national security concerns - have prompted South Koreans to boycott Japanese products and services including cars, beer and tourist trips.
However, industry watchers said public sentiment was a factor behind the sharp falls.
South Korea's government and ruling party have agreed to spend part of next year's draft budget on addressing Japan's tighter controls on exports to the country. It also warned them to be careful in visiting places in the country that are associated with Japan.
South Korean Prime Minister Lee Nak-yon on Sunday urged Japan to correct its "reckless and risky" decision to curb exports to the country, saying that the worldwide community is concerned about security in Northeast Asia after the latest developments. But they have also pointed to an erosion of trust after South Korean court rulings previous year ordered Japanese firms to compensate wartime forced laborers, a matter Tokyo says was settled by a 1965 treaty normalizing bilateral ties. The government aims to stabilize supply of these items over the next five years.
In Japan, the Ministry of Foreign Affairs warned Japanese citizens in South Korea to stay away from demonstrations.
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