Iijima, an adviser to Japanese Prime Minister Shinzo Abe who arrived in Pyongyang on Tuesday, met Thursday with Kim Yong Nam, the isolated Communist country's No. 2 leader after Kim Jong Un, the official Korean Central News Agency reported but gave no details.
Kyodo News, which carried the KCNA report, said Kim Yong Nam, president of the North Korean parliament, and Iijima were believed to have discussed ways to improve bilateral relations, including the resolution of North Korea's abduction of Japanese nationals in the 1970s and 1980s.
Song Il Ho, North Korea's ambassador for talks to normalize relations with Japan, attended the meeting, Tokyo-based Radiopress was quoted as saying.
Earlier, The New York Times reported Abe's office wouldn't even confirm Iijima's visit to North Korea. Japan and North Korea don't have formal diplomatic relations.
The purpose or the length of Iijima's visit had remained unclear. However, Kyodo quoted sources as saying the trip would end Friday.
It comes at a time when tensions on the Korean Peninsula remain high with North Korea continuing its saber rattling against the United States and South Korea.
The Wall Street Journal reported the unannounced visit might be designed to improve bilateral relations, coming in the wake of the easing lately by North Korea of its provocative statements and threats.
The visit also comes as Japan, the United States, South Korea and China have been talking to one another to end the North's belligerence, which worsened since the U.N. Security Council tightened sanctions against Pyongyang. The U.N. action came after North Korea, despite strong objections from the international community, conducted a nuclear test in February.
Iijima was also a top aide to former Japanese Prime Minister Junichiro Koizumi, who had twice met with the late North Korean leader Kim Jong Il. Kim Jong Il died December 2011 and his leadership role passed to his son Kim Jong Un.
The abduction issue is extremely sensitive in Japan and has been the main cause of tensions between Tokyo and Pyongyang. At least 17 Japanese nationals were reported to have been abducted in the 1970s and 1980s. Five were returned to Japan in 2002 and the North has maintained there are no other Japanese nationals in the country.
Last October, Kim Yong Nam in an interview with Kyodo, was quoted as saying the abduction issue had already been settled and that Japan should address the suffering of the Korean people during the 1910-1945 colonization of the Korean Peninsula.
Some analysts told Kyodo the North, by inviting Iijima, might be trying to frustrate coordination among Japan, the United States and South Korea and even China in dealing with the isolated country's long-range rocket and nuclear tests.
Earlier this month, Bank of China, the country's largest foreign exchange bank, was reported to have suspended business with North Korea's Foreign Trade Bank. That step was seen as a sanction by Beijing, which is the North's closest ally.
The visit of Iijima has apparently not been well received in South Korea.
Yonhap News reported the South Korean government described the visit as "unhelpful."
"It is important to maintain close coordination among the Republic of Korea (South Korea), the U.S. and Japan, toward North Korea," South Korean Foreign Ministry spokesman Cho Tai-young said. ""In that sense, we think that the visit by Iijima to North Korea is unhelpful."
The United States has been cautious in its reaction. State Department spokeswoman Jennifer Psaki said it would be impossible to comment "without knowing the specifics on the purpose of the visit."
Yonhap quoted some experts that Iijima's visit might also be look into the possibility of a summit between Abe and North Korean leader Kim Jong-un.
Biologists detail four new deep-sea 'killer sponges'
Pistorius testifies he didn't consciously pull trigger when he shot girlfriend