The police stopped the Taiwanese on Tuesday morning from marching to the shrine, even as a motley group of Japanese nationalists threatened to resist any attempt to delete the names.
"We want to take the spirits of our ancestors back to Taiwan," said Taiwanese politician Kao-Chin Su-mei, after police stopped the buses that carried the Taiwanese about 1km from the shrine.
"Japan is said to be democratic, but it is not," she said.
Even Taiwanese reporters who disembarked from the buses were stopped from approaching the shrine by the police, who said there was a possibility that the group's presence could lead to violence.
The 60 aborigines, many in traditional clothing, remained on the buses but held up signs to the windows reading "Apologise to your former colonies" and "Remove our ancestors' names".
Yasukuni Shrine is the final resting
place of Japan's war dead
Yasukuni Shrine is considered to be the last resting place of Japanese soldiers who died in battle, but attracts criticism from neighbouring countries that were invaded and colonised by Japan in the early decades of the last century.
Japanese nationalists, some in quasi-military attire and carrying the rising sun flag, said they would resist any effort to have the names of the estimated 27,800 Taiwanese who are enshrined at Yasukuni, removed.
"They should be quiet and keep out of this issue," said Sosaku Harada, 74. "This is a matter for Japan."
He said the Taiwanese volunteers had "fought alongside Japanese soldiers and should stay with them now".
Japan took over Taiwan in 1895 and controlled it as a colony until 1945. During the second world war, more than 25,000 people were conscripted into the Aboriginal Volunteer Army and sent to fight in New Guinea and the Philippines.
At the end of the conflict, the souls of those who had died in battle were enshrined at Yasukuni, alongside their former colonial masters and 14 Class A war criminals who were executed.
"We pray for the souls of the Taiwanese who died in the war just as we pray for the souls of Japanese soldiers here at Yasukuni," said Akihiko Kudo, a member of a nationalist group called Chiba Kenkoku.
"Ms Kao-Chin is saying that the Japanese government killed many Taiwan aboriginal people, but this is not true," he said. "We gave them schools and provided water. We gave them civilisation and I want her to stop telling lies."
But the Taiwanese protesters insisted they were right in seeking to "liberate" the souls of their ancestors from the Japanese shrine.
"We want to take the spirits of our ancestors back to Taiwan"
"We want to give a proper internment, in our own way, for our ancestors and liberate their souls from Yasukuni Shrine," Kao-Chin said. "And even though we have been blocked today, we will definitely return some day."
After being turned away from the shrine, the group
demonstrated outside the headquarters of Japan's bar association, singing a song calling for the return of their ancestors' souls.
In a rare show of support for Taiwan, a Chinese Foreign Ministry spokesman told reporters in Beijing that it supports the aboriginal peoples' claims.
"We believe that the wishes of our Taiwan compatriots are reasonable in terms of sentiment and logic and should be respected," Kyodo News quoted Liu Jianchao as telling reporters. "We hope the Japanese side will appropriately deal with this question left over from history."
Kao-Chin's group is scheduled to travel to Osaka later in the week to hear the ruling in a high court case she filed concerning Japanese Prime Minister Junichiro Koizumi's visits to the shrine.
Koizumi insists he would continue to pay his respects to Japan's war dead at the shrine and maintains that criticism from neighbouring countries, notably former colonies China and South Korea, amounts to interference in domestic affairs.