Lee's pilgrimage could take some of the glow off a rapprochement in Sino-Japanese ties, but analysts said its impact was likely to be limited.
China expressed ''strong dissatisfaction'' with Japan for allowing Lee to visit the country. ''Lee Teng-hui's behaviour in Japan shows what it is he aspires to,'' Foreign Ministry spokeswoman Jiang Yu told a news conference in Beijing.
She urged Tokyo to abide by agreements under which it recognises only one China.
Supporters of Lee, who was educated in Japan and led Taiwan from 1988 to 2000, shouted ''banzai'' (long life) when he arrived at the Shinto shrine's massive, tree-lined complex in central Tokyo. Some waved Japanese flags. Some shouted ''Taiwan forever''.
Yasukuni is seen by many in Asia as a symbol of Japan's past militarism. It honours millions of Japanese war dead - among them soldiers from Taiwan and Korea who fought for Japan, their colonial ruler at the time - but also some convicted war criminals, including wartime prime minister Hideki Tojo.
But Lee, 84, said his pilgrimage to Yasukuni was intended to pay respects to his elder brother, who died fighting for the Japanese during World War Two, when Taiwan was a Japanese colony.
''It is completely personal, please don't think of anything political or historical,'' he said, speaking in Japanese.
''As family, showing respect to my elder brother by visiting the shrine is something I must do,'' Lee said.
Japanese Chief Cabinet Secretary Yasuhisa Shiozaki said he foresaw no change in an expected meeting between Prime Minister Shinzo Abe and Chinese President Hu Jintao at this week's Group of Eight summit in Germany.
''It was Mr Lee's private act and it should not affect Sino-Japanese relations and I don't think it will,'' Shiozaki told a news conference.
SECONDARY MATTER Analysts said any damage to the fragile rapprochement that began after Abe took office last year was likely to be limited.
''China will find this hard to accept, but it doesn't represent any shift on Abe's willingness to open dialogue, and that's what China cares about,'' said Shi Yinhong, a regional security expert at the People's University of China in Beijing.
''Secondary things like this aren't going to change the course of relations,'' Shi added.
Relations had worsened under Abe's predecessor, Junichiro Koizumi, largely due to Koizumi's annual visits to Yasukuni.
Before becoming prime minister, Abe had backed Koizumi's visits to the Yasukuni shrine, but he has declined to say whether he would go there while in the country's top post.
Some diplomats said Lee's move was partly an appeal to conservative Japanese politicians who favour tighter ties with Taiwan, with which Tokyo has no formal diplomatic ties.
Beijing has claimed sovereignty over Taiwan since 1949, when China's Nationalist forces fled to the island after losing power on the mainland to Mao Zedong's Communists.
Many in Taiwan maintain a friendlier attitude towards Japan than those in mainland China, where many harbour deep resentment toward Tokyo due to wartime aggression and atrocities.
Taiwan was largely spared the harsh treatment meted out to many of the countries that Japan occupied during the war and many residents credit Japan for helping to modernise the island.
REUTERS GL RAI1515