Japan acknowledged the damage and suffering caused by colonial aggression across Asia with deep remorse, Koizumi said on Friday at the conference in Jakarta attended by Chinese President Hu Jintao.
"In the past, Japan, through its colonial rule and aggression, caused tremendous damage and suffering to the people of many countries, particularly to those of Asian nations," he said, but gave no mention of China.
"Japan squarely faces these facts of history in a spirit of humility. And with feelings of deep remorse and heartfelt apology always engraved in mind, Japan has resolutely maintained, consistently since the end of World War II, never turning into a military power but an economic power," he said.
Aljazeera's Tokyo correspondent, Fadi Salama, said that in addition to this latest apology, Japan had pledged compensation in the form of economic aid to countries in East Asia that were victims of Japanese aggression.
Koizumi, who hoped to meet Hu on the sidelines of the summit, added that his country was guided by the "principle of resolving all matters by peaceful means, without recourse to use of force".
In a speech given by Hu at the summit, Japan was also not mentioned.
"The purpose of Chinese foreign policy is to maintain world peace and common development"
Hu, speaking to an audience that included Koizumi, instead sought to reassure his country's poorer neighbours that despite China's economic success, it would not leave them behind.
"We solemnly reaffirm that China will follow steadfastly its chosen path of peaceful development.The purpose of Chinese foreign policy is to maintain world peace and common development," he said.
In Beijing, there was no official reaction on Friday to Koizumi's statement, Aljazeera's correspondent Izzat Shahrur said. Television and the Foreign Ministry's website made no mention of the apology.
Sino-Japanese relations are at one of their lowest ebbs in decades after three weekends of protests by tens of thousands in China against Japan's approval of a school textbook that critics say glosses over the country's wartime atrocities.
Demonstrators hurled bottles, eggs and rocks at Japan's diplomatic and business interests in China while calling for the boycott of Japanese products.
Japanese analysts have blamed their nation's diplomacy in part for sparking the demonstrations by neglecting sensitive issues, Aljazeera's Salama said.
Tokyo demanded Beijing's apology and compensation for damage caused by the protests, but China rejected the demands, saying the real issue was Japan's alleged denial of its wartime past.
Koizumi said on Friday: "Japan once again states its resolve to contribute to the peace and prosperity of the world in the future as well, prizing the relationship of trust it enjoys with the nations of the world."
"Japan once again states its resolve to contribute to the peace and prosperity of the world"
Japanese prime minister
Japan's post-war constitution, written by the United States, not only renounces war but forbids Tokyo from maintaining a military or even threatening the use of force.
However, Tokyo maintains what it calls self-defence forces, and Koizumi, a staunch ally of US President George Bush, dispatched 600 troops on a non-combat mission in southern Iraq.
The deployment, which began in December 2003, is Japan's first since the second world war in a country where fighting is under way.