President Yoon Suk Yeol accepted the resignation of National Intelligence Service director Kim Kyou-hyun, Yonhap reported, without giving further details.
Two other senior NIS officials also resigned, it added.
The string of resignations appear to be connected to personnel management issues that have been swirling at the spy agency since June this year, according to local media reports.
The changes come as North Korea is accelerating the development of its weapons programmes and earlier this week successfully placed its first military satellite into orbit.
Kim, a former deputy national security adviser and career diplomat, was appointed in May 2022 after Yoon's election victory.
Kim worked to "re-establish the reputation of the NIS as the country's top security and intelligence agency" in the period after Yoon's administration took over, the president's office said, according to Yonhap.
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