The official, who briefed reporters on condition of anonymity, says Japan told South Korea that it imposed the restrictions primarily because of unspecified "weaknesses" in South Korea's export control system. South Korea insists that its export controls are stronger than Japan's.
The two sides met Friday for the first time since Japan imposed the curbs last week.
South Korea says the restrictions on photoresists and other sensitive materials could hurt its economy and global supply chains.
That's according to Lee Ho-hyeon, a South Korean trade ministry official who briefed reporters on Friday after export officials from the two countries met in Tokyo for nearly six hours over the bitter trade dispute.
Lee says Japanese officials maintained Tokyo's stance that it won't negotiate over the trade curbs, which South Korea believes could hurt its export-dependent economy.
He says Japanese officials said, without specifying, that there have been "inappropriate" cases regarding Japanese exports to South Korea, but that they were unrelated to illegal shipments to a third country.
Japanese and South Korean officials are meeting in Tokyo to discuss Japan's tightening of controls on high-tech exports, a step that further strained relations between the two sides.
Friday's meeting is the first since Japan last week tightened the approval process for Japanese sensitive materials shipments to South Korean companies, citing inadequate management but without citing specific cases.
Japan also cited the absence of talks between the trade authorities, lack of trust and security risks while suggesting illegal transfers to North Korea. South Korea denies the allegations.
Japan's curbs are a blow to South Korea, as the world's biggest supplier of computer chips and displays used in TVs and smartphones needs the chemicals.
South Korea has sought Washington's help. Seoul sees Japan's curbs as retaliation for disputes over former Korean wartime labor.
South Korea has proposed an investigation by the United Nations or another international body as it continues to reject Japanese claims that Seoul could not be trusted to faithfully implement sanctions against North Korea.
Seoul's presidential office said Friday that South Korea has been thoroughly implementing U.N. sanctions against North Korea over its nuclear weapons program. It demanded that Japan to provide evidence for claims made by Prime Minister Shinzo Abe and his conservative aides that there may have been illegal transfers of sensitive materials from South Korea to North Korea.
Tokyo last week tightened the approval process for Japanese shipments of photoresists and other sensitive materials to South Korea, saying such materials can be exported only to trustworthy trading partners.