The agreement was reached between Japanese Prime Minister Yasuo Fukuda and visiting South Korean President Lee Myung-bak at their meeting in Tokyo.
The two also agreed to expand people-to-people exchanges and to have consultations regarding stalled talks on the bilateral economic partnership agreement, Kyodo news service reported.
This is the second meeting between the two since Lee took office in February.
Fukuda said he and Lee confirmed the need for North Korea to fully and accurately declare its nuclear activities as required under the six-nation talks on denuclearizing the Korean Peninsula.
Negotiations on the bilateral economic partnership agreement, which would go beyond a free-trade deal, have remained suspended since November 2004 after Japan rejected South Korea's demand that Japan further open up its market for agricultural products, the report said quoting a Japanese Foreign Ministry official.
Yonhap news agency reported Lee also met with Japanese Emperor Akihito and Japanese business leaders.