The so-called "2+2" talks will take place in Seoul next Tuesday between senior foreign ministry and defence ministry officials from both sides.
The resumption of the dialogue -- last held in 2009 -- hints at a slow thaw in practical diplomatic contacts despite a glacial rift in the overall relationship.
"At the talks, the first in more than five years, they will discuss defence and security policies and cooperation, regional security situations and other matters of mutual concern," the South Korean foreign ministry said in a statement.
Seoul called in the Japanese ambassador to protest after Tokyo's education ministry said all the textbooks would assert Japanese ownership of two separate island groups at the centre of disputes with China and South Korea.
The row between Seoul and Tokyo over a tiny set of South Korean-controlled islets has rumbled on for decades, in tandem with highly-emotive disputes related to Japan's 1910-45 colonial rule over the Korean peninsula.
Beijing and Tokyo have similar issues and the disputes are being highlighted as the region prepares to mark the 70th anniversary of the end of World War II.
South Korean President Park Geun-Hye and Chinese President Xi Jinping have already held two fruitful bilateral summits.
But Park has refused to sit down one-on-one with Japanese Prime Minister Shinzo Abe, while Xi has only managed a brief meeting with Abe on the sidelines of an APEC gathering in Beijing last year.
The rift between Seoul and Tokyo is particularly disturbing for the United States, which wants its two key military allies in Asia to be united in the face of an increasingly assertive China.
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