Kim was branded "anti-party and a counter-revolutionary member" by the country's State Security Department, after he exercised a "bad attitude" during North Korea's Supreme People's Assembly in June, the official said.
South Korea's Unification Ministry spokesman Jeong Joon Hee confirmed the execution during a press conference early on Wednesday, held to address media reports of a public execution of a senior-level North Korean official.
Two other senior officials were also punished in the past few months, the Unification Ministry said, although they escaped execution.
Kim Yong Chol, the head of North Korea's United Front Department, received "revolutionary punishment" at a rural farm, or hard labor, between mid-July and mid-August.
The United Front Department is the government body which manages dialogue and policies with South Korea.
He was accused of abuse of power, including "an overbearing manner and forceful push to strengthening authority into (the) Party's United Front Department," the South Korean official said. He is expected to return to his post.
Choe Hwi, a senior official with the Propaganda and Agitation Department of the Worker's Party, was also punished and has been undergoing "revolutionary re-education" in a rural area since late May, the South Korean official said.
Executions are widely considered a political tool for North Korean leader Kim Jong Un
to consolidate his hold on power.
In May 2015, the country's defense minister, Hyon Yong-chol
, was reportedly killed with an anti-aircraft gun after being accused of treason.
Two years earlier, Kim's uncle, Jang Song-thaek
, was executed after being branded a "traitor for all ages."