South Korea on Monday signaled plans to remove Japan from a list of countries with fast-track trade status from September, citing problems with export control measures.
Japanese Industry Minister Hiroshige Seko said Seoul had failed to show how Japan had purportedly fallen short of international export control measures.
"From the start, it is totally unclear under what basis South Korea can say that Japan's export control measures don't meet the export control regime," Seko said on Twitter.
The tighter trade regulations, including potential lengthy permit application processes, will apply to South Korean exports to Japan.
Japan announced earlier this month that it was removing South Korea from its own "white list" of countries that have enjoyed minimum trade restrictions, citing an erosion of trust.
Relations between the two countries have deteriorated since a ruling by South Korea's Supreme Court last year that Japanese companies should compensate South Koreans who were conscripted as forced laborers during World War Two.