The army colonel had handled espionage targeting South Korea at the North's General Bureau of Reconnaissance before arriving in Seoul last year, the South's Yonhap news agency said.
Unification and defence ministry spokesmen in Seoul confirmed the report but declined to give details such as the officer's name and exact date of defection. "He is the highest-level military official to have ever defected to the South," said a government official quoted by Yonhap.
The officer is believed to have given details about the bureau's operations against South Korea to authorities in Seoul, the unidentified official said.
The unification ministry spokesperson also confirmed a report by Dong-A Ilbo daily on Monday that a North Korean diplomat posted in an African nation had defected to Seoul last May with three family members.
The news came days after Seoul announced that a group of 13 North Koreans working in a state-run restaurant outside the country had fled to the South in a rare mass defection.
The group -- one male manager and a dozen women -- arrived in the South Thursday. They had reportedly been working at a restaurant in China's southeastern port city of Ningbo before coming to the South through a third country in Southeast Asia.
Seoul rarely confirms defections by North Koreans, especially senior officials, citing the potential threat to their safety. It also does not want to damage diplomatic relations with the countries through which they travel.
China is the North's sole major ally. Pyongyang reportedly has often lodged protests with transit nations used by defectors en route to Seoul.
The highly unusual disclosures prompted Seoul's main opposition party to accuse the government of trying to rally support among conservatives before Wednesday's parliamentary election.
The vote for the 300-seat national assembly is seen as a referendum on the policies of President Park Geun-Hye and her ruling conservative Saenuri Party. The unification and defence ministries denied political motives, saying the disclosures were made in the public interest.
In the past some defections were made public only after months of questioning and with the approval of the person concerned. This was out of consideration for the safety of their families in the North, said Cheong Seong-Chang of Seoul's Sejong Institute think tank.
"I can't help viewing these extremely rare disclosures... as attempts to influence the election," he said. The revelations came at a time of heightened military tensions on the divided Korean peninsula.
North Korea has condemned Seoul and Washington for spearheading a sanctions drive at the United Nations over its nuclear and missile programmes. It has also issued nuclear threats in response to annual large-scale military exercises which South Korea and the US began last month.
Nearly 30,000 North Koreans have fled poverty and repression in their country despite the risk of imprisonment and torture if caught, and settled in the South.
But the number of defectors -- who once numbered more than 2,000 a year -- has nearly halved since Kim Jong-Un took power in the North after the death of his father and longtime ruler Kim Jong-Il in December 2011.
Those who still manage to flee in recent years already have families settled in the South or are relatively well-off and well-connected members of the elite in search of better lives, according to experts and activists.
The highest-ranking North Korean defector to come to the South was Hwang Jang-Yop, the North's main ideologue and former tutor to Kim Jong-Il. He made a high-profile defection via the South Korean embassy in Beijing in 1997 and died in Seoul in 2010.
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