A North Korean soldier defected to the South on Saturday through the heavily militarised border, apparently shooting dead two superior officers in the process, the South Korean military said.

It is only the fourth such defection reported in the last 10 years, with none of the past incidents involving fatal shootings, and could raise already heightened tensions ahead of the South's presidential election in December.

"Six gunshots were heard and our guards spotted a North Korean soldier crossing the military demarcation line," a spokesman for Seoul's Joint Chiefs of Staff told reporters.

"Through loudspeakers, we confirmed he wanted to defect to the South and we led him to safety," the spokesman said, adding the soldier was being held in protective custody.

Under initial interrogation, the soldier said he had shot and killed his squad and platoon leaders before making his escape.

There was no independent confirmation of any casualties, but Yonhap news agency cited an unidentified military official as saying two North Korean soldiers had been seen "lying on the ground".

There was no immediate comment from Pyongyang.

Military defections across the land border between the two Koreas are rare, with the last reported crossing by a North Korean soldier in 2010, and previous instances in 2008 and 2002.

Once described by former US president Bill Clinton as "the scariest place on Earth", the Demilitarised Zone (DMZ) that divides the Korean peninsula between North and South was created after the 1950-1953 Korean War.

Four kilometres (2.5 miles) wide and 248 kilometres long, it is a depopulated no-man's land of heavily-fortified fences, bristling with the landmines and listening posts of two nations that technically remain at war.

Saturday's defection occurred at the only functioning transport link across the land border, a narrow road-and-rail corridor between the South and an industrial zone where southern companies have invested on the northern side.

South Korean soldiers in the area, on the western part of the frontier, were put on alert afterwards.

More than 23,500 North Koreans have escaped and resettled in the South since the end of the Korean War, but virtually all cross the North's border with China and most travel on to Southeast Asia in the hope of eventually reaching Seoul.

They face repatriation if discovered in China.

The latest defection comes at a sensitive time, with both Koreas trading accusations of provocative behaviour in the run up to the December 19 presidential election in the South.

"Apart from anything else, this is a real embarrassment for the North as the soldiers deployed along the border are supposedly the most loyal to (North Korean leader) Kim Jong-Un," said Yang Moo-Jin, a professor at the University of North Korean Studies in Seoul.

"The North will demand the soldier's immediate repatriation and the situation could easily escalate. In terms of any impact on the presidential election, it really depends how the South handles it," Yang said.

Last month, Seoul's navy fired warning shots to turn back North Korean fishing vessels after a series of incursions over their disputed Yellow Sea border.

A week later, South Korean President Lee Myung-Bak warned Pyongyang against any attempt to sway the presidential ballot and said the South's military would "retaliate strongly" against any provocative acts.

A few days later, a spokesman for the North's powerful National Defence Commission accused Lee's ruling conservative party of "war-mongering" in order to win votes.