The official added the situation is becoming less favorable to North Korea, and called on Pyongyang to respond to South Korea's offer of talks.
The man in his 20s was rescued on Gyodong Island near the Yellow Sea border at around 1 a.m. local time (1700GMT), local news agency Yonhap reported, citing the JCS.
Seoul's Unification Ministry is reportedly monitoring whether social instability in the North could be behind the leap in direct defections.
The northern resident was sent home via the inter-Korean truce village of Panmunjom, which sits in the demilitarized zone that separates the two countries.
After an interrogation, the South Korean government concluded the North Korean national wanted to return to North Korea.
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A young North Korean man made a perilous escape into South Korea via a border island Friday, according to Seoul's Joint Chiefs of Staff. The family reunion project materialized decades later, in a 2000 summit meeting between President Kim Dae-jung and North Korean leader Kim Jong-il, who agreed to regularly hold the humanitarian event.
The defection comes more than a month after a flurry of North Korea military desertions. South Korean officials noted the North "did not show any special reaction". The soldier reportedly used blocks of Styrofoam as floats for his back and shoulders to survive the unsafe swim.
The four men and one woman were spotted in the sea northeast of Gangneung city, Gangwon Province near the inter-Korean border.