Reports tell us that JP government officially determined that Kim Jon Il were aware of the kidnapping, although he denied his involvement in his meeting with former PM Koizumi.
http://www.asahi.com/english/Herald-asahi/TKY200911030097.html

Kim Jong Il oversaw abduction agency

THE ASAHI SHIMBUN

Japanese government officials have determined that North Korean leader Kim Jong Il oversaw the Pyongyang agency responsible for abducting Japanese nationals in the 1970s and 1980s, despite Kim's claim he was not involved, sources said.

The officials believe Kim either ordered the abductions or at least was in a position to know about them, the sources said.

When Kim admitted to then Prime Minister Junichiro Koizumi in September 2002 that North Korean agents had abducted Japanese nationals, he indicated he had not been connected to the operations.

He said they "were carried out by elements within a special agency that turned toward impulsive, and what they considered heroic, acts." The party had disciplined the agents responsible, Kim said.

This new revelation will make it more difficult for Prime Minister Yukio Hatoyama to carry out his plan to normalize relations with North Korea. The outcome of that plan will hinge largely on his ability to resolve the abduction issue, and concurrently make a breakthrough on the issue of North Korea's nuclear weapons and missile development programs.

An overseas intelligence investigation division under the ruling Workers' Party of Korea carried out the abductions of Japanese nationals from the 1970s to the early 1980s.

The investigation by Japanese government officials has determined the division, now called Room 35, reported directly to Kim, who at that time was solidifying his position as eventual successor to his father, Kim Il Sung, who died in 1994.

The division comprised a director and three deputy directors as well as section chiefs, supervisors and agents.

It was made up of seven sections, some of which were assigned to work exclusively on individual countries, such as Japan, South Korea and China.

When they would receive instructions from Kim, the director, deputy directors and section chiefs met for ceremonies at the Workers' Party of Korea headquarters.

At the ceremonies, a document was read that usually began with wording such as "Dear General, Comrade Kim Jong Il made the following observations." The instructions that followed were issued in writing or verbally.

The section chiefs would then relay them to the supervisors and the supervisors to the agents. The party would discipline anyone who disobeyed these orders. Disciplinary measures included dismissing them from their posts and executing them.

Japanese police officials have already determined that Li Wan Gi, former director of the overseas intelligence investigation division, and Kan Hae Yong, a former deputy director of the same division, were involved in the planning and supervision of the abduction of Yasushi Chimura and his wife Fukie, as well as Kaoru Hasuike and his wife Yukiko. The two couples returned to Japan in 2002 along with Hitomi Soga.

Government sources said police officials at one time considered seeking arrest warrants against Li and Kan, but that plan was shelved by people close to then Prime Minister Yasuo Fukuda.

According to diplomatic sources, in February 2008, Japanese government officials questioned Choi Un Hee, a South Korean actress who was abducted to North Korea in 1978 and later escaped. Choi said that by the 1970s Kim had taken over management of the government from his father. She believed he gave the order to abduct Japanese nationals.(IHT/Asahi: November 3,2009)