Seko said the curbs "were a consequence of South Korea failing to present satisfactory measures" to resolve the issue of South Koreans forced to work for Japanese firms during World War Two, he said.
"All trade-related actions by Japan are in line with the WTO rules," said Seko, speaking to reporters after a regular cabinet meeting.
"Because our (mutual) trust has severely damaged, we have judged it is difficult to ensure proper export controls are being taken."
Japan is tightening curbs on exports of three materials used in smartphone displays and chips to South Korea amid the growing dispute over wartime forced labor.
South Korea has denounced the measure as a violation of WTO rules, saying it would take the necessary countermeasures including filing a complaint with the organization.