On Thursday, the ministry released five photos of the flyby to substantiate its assertion that the Japanese P-3 maritime patrol plane buzzed Korea's 4,500-ton destroyer Daejoyeong at an altitude of 60 to 70 meters and just 540 meters away in international waters south of the peninsula Wednesday.
According to Japan's Asahi Shimbun, a senior Tokyo official discredited the photos, saying his government has "proper" evidence of its own to repudiate Seoul's position.
"If Japan believes that the things we released cannot serve as proof to back up our position, it has to provide evidence to explain why it thinks so," an official at the ministry told reporters.
The latest flyby further aggravated tensions amid a lingering bilateral dispute over Seoul's naval radar operation last month.
This week's incident is the third of its kind this month alone.
Japan's military aircraft flew close to Korea's 7,600-ton Yulgok YiYi destroyer last Friday and to the 4,500-ton Nojeokbong landing ship on Tuesday.
Seoul called Wednesday's flyby a "clear provocation" and vowed to deal sternly with such an incident.
Later in the day, South Korea's Vice Foreign Minister Cho Hyun called in Yasumasa Nagamine, Japanese ambassador to South Korea, to express regret over the Japanese military's low-altitude flyby, a ministry official said.
"They exchanged opinions over diplomatic relations between the two nations, including the Japanese patrol plane's flyby," a ministry official said without elaboration, asking to be unnamed. (Yonhap)