In this Dec. 22, 2010, file photo, a government ship sails past the South Korean Navy's floating base as the sun rises near Yeonpyeong island, South Korea. AP

North Korea shot a missing South Korean official to death and burned his body earlier this week, the defense ministry confirmed Thursday, condemning its "brutality" and calling for explanations and punishment for those responsible.

The 47-year-old official affiliated with the Ministry of Oceans and Fisheries disappeared from the 499-ton boat before noon Monday while on duty aboard an inspection boat in waters off the western border island of Yeonpyeong.

"North Korea found the man in its waters and committed an act of brutality by shooting at him and burning his body, according to our military's thorough analysis of diverse intelligence," the defense ministry said in a statement.

"Our military strongly condemns such a brutal act and strongly urges the North to provide an explanation and punish those responsible," the statement read. "We also sternly warn North Korea that all responsibilities for this incident lie with it."

It is the first time since July 2008 that a South Korean civilian has been shot dead in North Korea. At that time, Park Wang-ja was shot and killed at the North's mountain resort of Kumgang while wandering into a restricted zone.

The incident is expected to further deteriorate inter-Korean relations that have already been frayed badly, as the North angrily protested propaganda leaflets flying in from the South and blew up an inter-Korean liaison office building in June.

According to officials of the South's Joint Chiefs of Staff, the missing official is presumed to have jumped into the sea Monday in a suspected attempt to defect to the North and had drifted into North Korean waters.

The ministry earlier said that colleagues of the fisheries official found his shoes on the boat and reported his disappearance to the Coast Guard. But an intensive search operation failed to find him.

Upon spotting the individual at sea at around 3:30 p.m. Tuesday, sailors of a North Korean vessel put gas masks on and questioned him from a distance while leaving him in the waters. The South Korean was wearing a life jacket and relying on an unidentified floating item.

He was found in waters about 3 to 4 kilometers north of the Northern Limit Line (NLL), the de facto inter-Korean maritime border, near Deungsangot, or Deungsan Cape, and the location was about 38 kilometers from where he went missing, according to the JCS.

During the questioning, the South Korean official appears to have expressed his desire to defect to the North, according to a JCS official.

"At around 9:40 p.m., the North Korean soldiers aboard their vessel shot him before pouring oil over his body and setting it aflame at around 10 p.m.," the JCS official said, adding that the act was believed to have been done in accordance with "orders from its superior authority."

South Korean surveillance equipment set up on Yeonpyeong Island also captured flames Tuesday night, which were later confirmed to have been from the North's burning of the body.

"We judge that North Korea appears to have done such acts against humanity of unconditionally shooting an individual as part of its COVID-19 quarantine guidelines," the official said.

North Korea has made all-out efforts to stave off the new coronavirus. Pyongyang claims there has not been a single case there, and the country closed its border with China in January and implemented the maximum emergency level against the virus in July.