Monday's meeting was requested by the North which said it wanted to discuss the operation of military-to-military hotlines, some of which have fallen into disrepair.
The hotlines are intended to avoid misunderstandings between the two sides which remain on a constant state of military readiness and regularly train for all-out war.
South Korean officials said they would brief reporters on the outcome of the talks later on Monday.
Despite the planned meeting, North Korean media has stepped up its rhetoric against the South in recent days, warning that relations have "reached an extremely dangerous phase".
In a commentary over the weekend, North Korea's Rodong Sinmun newspaper attacked what it called the "treacherous" policies of the South Korean president and his associates which it accused of planning a "pre-emptive strike" against the North.
|North Korean media has accused the South of preparing for war [GALLO/GETTY]
"The Lee group is getting frantic in its war moves," the newspaper said, adding that conditions had become "so tense war may break out on the Korean Peninsula any moment".
More than 50 years after being divided, North and South Korea remain technically at war, never having signed a formal peace treaty ending the 1950-53 Korean War.
Earlier this month, military officials from North and South Korea failed to make any progress in colonel-level talks - their first official contact since Lee took office.
During that meeting, the North Korean delegation protested over leaflets critical of its leader, Kim Jong-il, sent over the border by private activists in South Korea.
The leaflets, numbering in the hundreds of thousands, are transported by balloons launched from boats sailing near the border.
In response North Korea has threatened to expel South Koreans working at a joint industrial zone in the North unless the leaflet drops are halted.
The subject was expected to come up again during Monday's talks.
More than 70 South Korean companies employ about 32,000 North Korean workers producing clothes, utensils, watches and other labour-intensive goods at Kaesong, an industrial town just across the border.
In 2004 officials from North and South Korea agreed to end decades of fierce propaganda battles which often used leaflets and messages over powerful loudspeakers sent over their shared border.
The South Korean group behind the latest leaflet drops, Fighters for Free North Korea (FFNK), says it has no plans to halt its operations and planned to send a further 100,000 leaflets across the border on Monday, with more to follow at a later date.
FFNK leaders say that apart from denouncing the North Korean government, they also want the North to come clean over the fate of hundreds of South Koreans abducted during the Cold War.