Takeshi Iwaya met counterpart Cho Tae-yul for discussions in the capital Seoul, the South Korean foreign ministry said, with the two later holding a news conference.
It is the first such meeting by Tokyo's top diplomat in Asia's fourth-biggest economy for more than six years.
Cho said the ministers had "expressed strong concerns over North Korea's nuclear and missile development", in particular Pyongyang's growing military ties with Moscow, including troop deployments.
The talks also focused on trilateral cooperation with mutual ally the United States -- before Trump, who has previously questioned the US's Asian security alliances, takes office on January 20.
The three nations have bolstered security cooperation in recent years, including sharing information on North Korean missile launches.
The latest such test was last week when Pyongyang said it had fired a new hypersonic missile, the same day US Secretary of State Antony Blinken was visiting Seoul.
Cho said he and Iwaya had agreed on "the necessity of continued close coordination among Korea, Japan, and the United States to counter the North Korean nuclear threat".
Tokyo and Seoul's bilitaral ties would also continue to be developed "under any circumstances", with diplomacy to "remain consistent and unwavered", he added.
Iwaya is scheduled to meet acting president Choi Sang-mok on Tuesday, the Japanese government said.
AzVision.az
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