It was Koizumi's fourth annual visit to Tokyo's Yasukuni Shrine since taking office in April 2001 and his first on New Year's Day, when millions of Japanese make their first visits of the year to Shinto shrines and Buddhist temples.
The Shinto shrine is seen as a symbol of Japan's early 20th century colonialism and military aggression.
Yasukuni is where the souls of more than 2½ million Japanese who have died in foreign wars since 1853 are said to be enshrined, including Class-A war criminals from the Second World War.
Junichiro Koizumi (left) follows chief Shinto preist in Tokyo (AP photo)
In Beijing, China's Vice-Foreign Minister Wang Yi lodged a strong diplomatic protest. He called the visit an act of broken faith and said the Chinese people will never tolerate it. The reaction is seen as dimming the chances of an anticipated trip to China by Koizumi or for China's president to travel to Japan any time soon.
In Seoul, South Korea's Foreign Ministry said it deeply regrets the prime minister paying homage to war criminals who inflicted intolerable damage and pain on the Korean people.
At the shrine, Koizumi, anticipating the foreign protests, said, essentially, Asian neighbours should get used to it.
The prime minister told reporters that each nation has its own history and tradition and other countries should be able to understand that.
The visit also was met by opposition from one of the parties in Koizumi's governing coalition. The head of the party has expressed regret and questioned whether the visit violates the constitutional prohibition against the state engaging in religious activities.
Koizumi said he made the trip as a private individual and even paid the equivalent of about $250 Cdn out of his own pocket to buy flowers. However, he acknowledged that he signed his name in the visitors book as prime minister.
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