South Korean defence officials had said before Thursday's meeting that the two sides would focus on discussing the implementation of previous defence agreements.
|Hill is in Pyongyang on a mission to salvage the stalled nuclear deal [AFP]
"We are holding talks at a time when North-South ties are at a very grave state," said Pak Rim-su, a North Korean delegate, according to a pool report.
The talks, proposed last month by North Korea, took place a day after South Korea held a major military parade, and amid North Korean threats to restart its nuclear programme.
On Wednesday South Korea's president marked Armed Forces Day by urging the military to be "prepared to deal sternly with any forces that threaten our security".
"Only a strong military can defend our land, deter war and guarantee peace," Lee said in a televised speech.
"Even if the enemy tries to invade us, we have to give our people trust that we are definitely going to win."
North-South relations warmed significantly after the first-ever summit of their leaders in 2000, and a second summit held exactly a year ago, but quickly deteriorated after Lee assumed the presidency.
North and South Korea remain technically at war never having signed a peace treaty ending the 1950-53 Korean War, which killed millions of people and left the peninsula divided.
Thursday's meeting also came amid heightened tensions over Pyongyang's move to restart nuclear facilities and concerns over the health of Kim Jong-il, the North Korean leader.
Christopher Hill, the chief US negotiator to six-party talks on the North's nuclear programme, who is in Pyongyang, will offer a face-saving compromise to try to rescue the stalled nuclear deal, US officials confirmed on Thursday.
The US state department said Hill will hold more talks with North Korean officials before returning to South Korea. He will be heading to China on Friday.
Sean McCormack, a department spokesman, gave no details of Hill's trip except to say that Beijing could play the "special role" it has in the past "as a repository for documents and information".
China has hosted six-nation talks on North Korea's nuclear programme, with partners South Korea, China, Japan, Russia and the US.