Dozens of protesters surrounded by hundreds of riot police marched through the city, which hosted the 1998 Winter Olympics, carrying Tibetan flags and banners saying "Stop the Torch" as the flame arrived. Police helicopters buzzed in the air.
Police arrested a 47-year-old man claiming to be a monk for allegedly possessing a short sword and a written statement opposing the torch relay at the starting point of Saturday's event, a local police official said on condition of anonymity, citing policy.
The torch has been met with protests and intense security at many of its stops on its worldwide journey, and Japan was gearing up for yet another game of cat-and-mouse between police and demonstrators demanding better human rights in China and condemning Beijing's crackdown on Tibetan protests last month.
In a last-minute change, the 11.6-mile torch relay was to begin in a parking lot at 8:30 a.m. Saturday (2300 GMT Friday) instead of an ancient temple. Zenkoji temple declined last week to host the start of the relay, citing security concerns and sympathy among monks and worshippers for their religious brethren in Tibet.
The 1,400-year-old temple also announced it would co-host a prayer ritual for Tibet on Saturday.
Five tracksuit-clad riot police will run alongside the torchbearers, who will also be followed by two Chinese officials. Phalanxes of 50 riot police will surround the torch on the right and left. About 3,000 police have been assigned to security.
Groups including Amnesty International and Reporters Without Borders have announced plans to protest.
"We will try to get as close as possible to the pathway of the torch, but the aim is to really to have a peaceful demonstration," Robert Mendard of Reporters without Borders told reporters Friday evening in Tokyo before heading for Nagano.
Mendard, however, said he plans to stop the protest "if it is confirmed tomorrow that there is truly a dialogue between the Chinese authorities and Tibet."
About 2,000 Chinese exchange students, meanwhile, were expected to arrive in Nagano by bus to show their support.
Japanese officials called for calm.
"In a festive environment where everyone can celebrate, we hope the Olympic torch relay will proceed smoothly," Chief Cabinet Secretary Notubaka Machimura told reporters in Tokyo.
Besides the protests in Nagano, a handful of young people raised the flag of Tibet's exiled government Friday at a highway rest stop when the caravan carrying the torch pulled over. There were no confrontations.
After Nagano, the Olympic torch heads to Seoul, South Korea, on Sunday and then to Pyongyang, North Korea, on Monday.
A U.S.-based group, Human Rights Watch, urged South Korea on Friday to use the torch relay to highlight the plight of North Korean refugees in China.
Thousands of North Koreans are believed to be hiding in China after escaping their impoverished communist homeland. If caught, China sends them back to North Korea, where they face imprisonment in conditions that are often life-threatening.
The torch next travels to Vietnam, which expelled an American citizen of Vietnamese origin who planned to disrupt the relay there, state media reported Friday.
Vuong Hoang Minh, 34, was put on a flight back to the United States on Thursday, the Vietnam News Agency said. It said Minh told authorities he planned to snatch the torch.
A spokeswoman at the U.S. Consulate General in Ho Chi Minh City confirmed that Minh was sent back to the United States, but was unable to say why he was deported.
From Vietnam the torch heads to Hong Kong.