Sino-Japanese ties chilled during Junichiro Koizumi's 2001-2006 term as Japanese prime minister, when he outraged Beijing with his visits to Yasukuni Shrine for the war dead, seen in much of Asia as a symbol of Japan's past militarism.
Ties have since improved, and experts said the main purpose of what is only the second state visit by a Chinese leader was to cement a shift to friendlier ties by the Asian rivals, closely linked by trade and investment despite rows over the past.
"The fact that the visit is taking place is an achievement," said Andrew Horvat, a professor at Tokyo Keizai University.
Many ordinary citizens in both countries, though, are wary of the other nation, while anti-Chinese feelings among some Japanese have been stirred by Beijing's reaction to Tibetan unrest.
"I just want to say 'Free Tibet'. I want to say 'No' to China's oppression of human rights," said 29-year-old Atsushi Hanazawa, who carried a guitar along with a Tibetan flag.
About two dozen right-wing activists yelled anti-Chinese slogans such as "Hu Jintao, Go Back to China". Earlier, some right-wing Waseda alumni protested against Hu's speech in a blog.
Nationalist Japanese have seized on Tibet as an issue to vent their anti-Chinese feelings.
Nearby around 50 Chinese students held their own rally, yelling "Go, China" in Chinese, "Sino-Japanese Friendship" in Japanese, and "Yes, We Can" in English. "I love President Hu," some shouted.
"When I hear the anti-Chinese slogans, I feel that the Chinese people's character has been maligned," said 28-year-old Chinese graduate student Cao Shunrui.
Hu is also seeking to convince his own sceptical citizens that the two nations should draw closer, and on Thursday he stressed that his country had much to learn from Japan.
His praise of Japan and call to bear no grudges from history were widely report by state-run Chinese media.
"Hu's visit is also undoubtedly meant as education and encouragement for China's people too -- to show that Japan can be a partner," said Shi Yinhong, a regional security expert at Renmin University in Beijing.