Braving the rainy morning, Koizumi, dressed in a business suit rather than traditional Japanese clothing, offered a silent prayer in front of the offering box without entering the main hall, the Asahi Shimbun reported. He did not respond to reporters' questions as he left the shrine.
Monday was the beginning of autumn memorial services at the shrine.
It was Koizumi's first visit to the site where Japan's war dead are enshrined since New Year's Day last year, and his fifth since becoming prime minister in April 2001.
Wang Yi, China's ambassador to Japan, said Koizumi's act was a "grave provocation" to the Chinese people, and Koizumi must take responsibility for damaging China-Japan relations, China News Service reported.
South Korean Foreign Minister Ban Ki Moon summoned Japan's ambassador to Seoul, Shotaro Oshima, to say his government felt "deep regret and disappointment" over the shrine visit.
Japan's Chief Cabinet Secretary Hiroyuki Hosoda told reporters the visit was made in a private capacity. Koizumi has repeatedly said he visits the shrine to honor the country's war dead and to pledge Japan will not go to war again.
The visits are controversial even in Japan, where business people in particular fear they will harm economic dealings with their neighbors, especially China.