Acting Press Secretary Silvestre Afable, in a tele-conference with reporters at Malacañang, said the Japanese premier and Mrs. Arroyo met for 30 minutes at Koizumis office in Tokyo.
The President welcomed Japans increased contribution to regional security.
Japan, whose military power is a sensitive issue in Asia where Japanese forces invaded countries such as the Philippines, China and Korea during World War II, now provides logistics support for US forces in Afghanistan.
"We welcome the new role, the increased role of Japan in assisting, in promoting security in the region," Mrs. Arroyo said.
The President is on the second day of her four-day working visit to Tokyo upon the invitation of the Nihon Keizai Shimbun, Japans leading financial newspaper.
For her part, Mrs. Arroyo congratulated Koizumi for his outstanding leadership that enabled Japan to attain economic recovery from recession.
Afable, who was a member of the Presidents official party, said Mrs. Arroyo also thanked Koizumi for Japans assistance to the development of Mindanao which she said was a big boost to solving the islands terrorism and insurgency problems.
Afable said the President also impressed upon the Japanese leader her belief that developed countries like Japan should help developing nations such as the Philippines combat terrorism and criminality by addressing poverty.
"One of the most important statements the President has been making here is that after the Cold War and the Second World War, there are no more threats from strong states," Afable said.
He added that the threats come from poor nations that are becoming the spawning grounds for terrorism.
Mrs. Arroyo also batted for an Economic Partnership Agreement (EPA) between Manila and Tokyo patterned after a similar pact between Japan and Singapore.
Afable said the proposed EPA would cover not only bilateral trade relations, but also cooperation in science and technology, human resource development and information and communications technology. Marichu Villanueva