"In a festive environment where everyone can celebrate, we hope the Olympic torch relay will proceed smoothly," Nobutaka Machimura, the chief cabinet secretary, said in Tokyo.
On Friday a handful of young protesters raised the flag of Tibet's exiled government in a peaceful protest at a highway rest-stop parking lot when the caravan carrying the torch pulled over.
Dozens more demonstrators protested against the flame near the vacant lot where the flame relay was to begin early on Saturday.
Groups including Amnesty International Japan and Paris-based Reporters Without Borders have said they both plan to stage a protest.
On Friday Kunio Hatoyama, Japan's justice minister, said immigration procedures have been tightened but there were no grounds to bar the entry of human rights activists.
The torch relay has sparked protests at nearly every stop on its trek around the world over China's violent crackdown in Tibet in March.
The Australian leg ended on Thursday without serious disruption, but nonetheless saw scuffles between pro-China supporters and pro-Tibet protesters.
Several people were detained during the massive security operation in the Australian capital, Canberra.
Last week a leading Buddhist temple in Nagano announced it was pulling out of plans to host the start of the relay, citing security concerns and sympathy among monks and worshippers for their Tibetan brethren.
The 1,400-year-old temple also announced it would co-host a prayer ritual for Tibet on the morning of Saturday's relay.
After Nagano, the Olympic torch will head to the South Korean capital, Seoul, on Sunday before moving north to Pyongyang on Monday.