Japanese Foreign Minister Hirofumi Nakasone and his counterpart Yu Myung-Hwan discussed a series of recent threats from the North, including a declaration that it is scrapping all peace accords with Seoul.
"Both ministers share the view that tension created by a series of North Korea's recent strongly worded comments is not helpful, and urged North Korea to act in a way to contribute to stability in the region," according to a South Korean statement after the ministers met.
The North has stepped up its attacks on Seoul's conservative government, fuelling fears of naval clashes along their disputed Yellow Sea border.
Pyongyang's military has said it is adopting "an all-out confrontational posture to shatter" the Seoul government.
Last week US and South Korean officials said the North appeared to be preparing to test-launch its longest-range missile.
Pyongyang also has hostile relations with Tokyo, which is pressing the North to account fully for the Japanese it kidnapped during the Cold War era.
Yu told a press conference after the talks that Seoul would soon arrange a meeting between the family of a Japanese woman abducted in 1978 and a former North Korean spy now living in the South.
The ex-spy, Kim Hyun-Hee, has said she saw Yaeko Taguchi in the North in 1987, one year after the North's regime said she died in a car crash.
"I feel I got very good support, as Minister Yu reaffirmed that he would cooperate and back Japan's position on the abduction issue," Nakasone said.
Nakasone said he and Yu had "in-depth" talks on North Korea. Their two countries, along with China, the United States and Japan, are members of a six-nation forum trying to negotiate nuclear disarmament with the North.
The talks are stalled by a dispute over how to verify Pyongyang's atomic activities.
The ministers met as the new US administration formulates its policy on North Korea. US Secretary of State Hillary Clinton makes her inaugural East Asian trip next week.
"To achieve peace and stability in Northeast Asia, I pointed out it is necessary to comprehensively resolve the nuclear issue, the missile issue and also the human rights issue including the abduction issue," Nakasone said.
He stressed the need for close cooperation between Japan, South Korea and the United States in the six-party process, adding the issue will be discussed when Clinton visits.
Nakasone's press secretary Kazuo Kodama, in an evening briefing, urged the North not to go ahead with its reported missile test plan.
"I would like to emphasise that the (North) should not test-launch ballistic missiles. It's in nobody's interest," Kodama told reporters.
Relations between South Korea and former colonial power Japan have often been prickly, but their leaders at a summit last month sidestepped historical and territorial disputes and vowed to develop a "future-oriented" partnership.
The ministers said Wednesday they would push ahead with a planned joint reconstruction effort in Afghanistan involving job training, education and an agricultural project.
They also pledged to work together at a G20 summit in April to revitalise the world economy and prevent the spread of trade protectionism.