"We can't help deploring and expressing anger at the prime minister's visit to the Yasukuni shrine... Despite concerns and warnings by neighbouring countries," Seoul's culture minister Yoo Jin-Ryong told reporters.
"The visit... Is an anachronistic behaviour that fundamentally damages not only relations between the South and Japan but also the stability and cooperation of the northeast Asia," he said.
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The comment came hours after Abe made his first visit to the Yasukuni shrine -- the believed repository of around 2.5 million souls of Japan's war dead including several high-level war criminals -- since taking office last December.
South Korea and China see it as a symbol of Tokyo's unrepentance for the horrors of last century and say it whitewashes the country's warmongering past.
Yoo said the shrine honoured those who inflicted "indescribable" pain and suffering on Koreans during Japan's 1910-45 occupation of the peninsula.
"Japan, if it genuinely seeks to make active contribution to the world peace, first needs to build trust with the neighbouring countries... Through thorough self-reflection and apology... Instead of denying its past and glorifying past aggressions," he said.