Former North Korean agent Kim Hyon Hui left Japan on Friday afternoon for South Korea, completing a four-day visit during which she met with relatives of Japanese abducted by Pyongyang.
Kim departed from Tokyo's Haneda airport aboard a Japanese government-chartered plane at around 3:30 p.m.
While the 48-year-old Kim, responsible for downing a Korean Air airliner in 1987, did not provide fresh information on the abductees' status, Chief Cabinet Secretary Yoshito Sengoku said Friday her visit was "very meaningful."
"I know there are many evaluations of this visit," Sengoku said at a news conference.
"But I believe it has helped many people in the country to develop a strong indignation and interest regarding the abduction issue, which represents a violation of human rights and national sovereignty."
After arriving in Tokyo early Tuesday, also aboard a government-chartered plane and under heavy security, Kim was flown by helicopter to former Prime Minister Yukio Hatoyama's country house in Karuizawa, Nagano Prefecture, where she met with relatives of abductees Yaeko Taguchi and Megumi Yokota.
Kim moved to Tokyo on Thursday and met with relatives of other abductees, and dined with lawmakers.
The special treatment accorded to her by the government, including her stay in the summer resort home and travel by helicopter, have been criticized by a number of opposition lawmakers.
But Sengoku defended the tight security measures that have been enforced as providing "the quietest possible environment" for her meetings.
Sengoku also said he is not aware of how much the government spent on Kim's visit.