Some of the demonstrators held banners calling for a "Free Tibet".
There were no reports of arrests.
After a dinner with Fukuda, Hu was to meet Emperor Akihito and then take part in a summit meeting on Wednesday.
Later in the day, Hu was to meet business leaders and the heads of Japan's main political parties.
Japan's foreign ministry said China will agree in an expected joint statement on global climate change to consider ways to help halve global greenhouse gas emissions by 2050.
The five-day trip is intended to build on a friendlier turn that relations have taken after years of friction over disputed borders, Japan's treatment of its wartime invasion of China, anti-Japanese protests in China and general Japanese unease over Beijing's rapidly growing diplomatic, military and economic power.
"There is a wide range of issues to talk about, not only Japan-China relations but also peace and stability and economy in the region, and I hope we can exchange views from a broad perspective," Fukuda said.
But, to set a friendly tone, they were also expected to play pingpong and discuss pandas.
Ling Ling, a beloved 22-year-old giant panda at Tokyo's largest zoo and a symbol of friendship with China, died last week of heart failure.
"It would be nice if we have a panda there again," Fukuda said last week.
Message to Japan
For Hu, the visit is a chance to portray China's role as a friendly, good neighbour after weeks of protests over Tibet and human-rights issues that dogged China's worldwide Olympic torch relay.
In a message to Japanese readers in the Japanese-language magazine People's China, Hu said: "I sincerely hope the people of the two countries can maintain friendship generation after generation and create a brighter future for the Sino-Japan friendship."
Hu said he expected the tone of his visit to be like a "warm spring", and that he was "looking forward to meeting with my old Japanese friends and making more new friends".