In a sign of how troubled the relationship is, Wednesday's meeting was sunk because the two sides disagreed about what should be on the agenda of their next talks - what many had hoped would be the first high-level defense talks in years.
On Wednesday, South Korea argued the high-level talks should focus on two attacks against it last year, while the North Koreans demanded discussion of other military issues as well, South Korea's Defense Ministry said in a statement.
South Korea blames the North for a warship sinking last March that killed 46 sailors, though North Korea flatly denies its involvement. Tensions sharply escalated further in November when the North launched an artillery barrage on a front-line South Korean island, killing four people.
In the midst of the back and forth, officers from the North abruptly walked out and no date was set for another meeting, a Defense Ministry official from the South said on condition of anonymity, citing department policy.
In Washington, U.S. State Department spokesman P.J. Crowley said that it was a "missed opportunity" for North Korea to demonstrate its sincerity to engage in dialogue and reduce tensions on the Korean peninsula.
He told a news conference the North needed to take "meaningful steps" to improve inter-Korean relations - including taking responsibility for the island shelling and warship sinking.
The fact that the two Koreas could not decide on an agenda shows how difficult the relationship has become in the past few years, after South Korean President Lee Myung-bak's administration took a harder line with the North.
Efforts to make real progress on a variety of issues - the North's nuclear program, a series of joint industrial projects and tourism - are often stalled before they even really begin. And when disagreements at meetings like Wednesday's aren't derailing progress then aggression from the North is.
While no date has been set for the rivals to speak again, all is not lost. The two sides did manage to agree to discuss restarting reunions for families separated by the 1950-53 Korean War. Eventual talks on that issue could provide an opening for wider discussions.
Improving relations between the Koreas and hopefully, in turn, bringing North Korea back into the fold of the international community is so important because of concerns about the North's expanded nuclear capability. South Korea says the North's newly disclosed uranium enrichment program violates disarmament pacts and U.N. resolutions.
The revelation has put pressure on the international community to get North Korea back to the negotiating table on its nuclear program. But, at the same time, the U.S. and South Korea want to see a commitment from the North that it's really ready to give up its weapons program - which its recent behavior has called into question.
Associated Press writer Matthew Pennington contributed to this report from Washington.