Mrs Kadeer said China's ethnic minority policies had failed
China has summoned Japan's ambassador in Beijing to protest about a visit to Japan by Uighur activist Rebiya Kadeer.
Mrs Kadeer, the head of the Uighur World Congress, is in Tokyo, where she has met members of the governing party.
Beijing accuses Mrs Kadeer, 62, of inciting ethnic violence in western China this month that left nearly 200 people dead - an allegation she denies.
China has also complained to Australia about Mrs Kadeer's forthcoming visit there, officials say.
She is due to attend a film festival in Melbourne next week, and will give a televised speech.
Japanese Ambassador Yuji Miyamoto was summoned to hear China's "strong dissatisfaction" over Mrs Kadeer's visit, said the Chinese foreign ministry.
China's Vice-Foreign Minister, Wu Dawei, said Beijing "demanded the Japanese government immediately take effective measures to deter [Mrs Kadeer] from engaging in anti-China separatist activities in Japan".
Beijing holds that Mrs Kadeer, who lives in exile in the US, was behind the violent unrest in western Xinjiang province earlier this month.
Violence broke out in Urumqi on 5 July between the Uighurs and the Han Chinese. The clashes continued for several days.
On Tuesday, Mrs Kadeer met members of Japan's governing Liberal Democratic Party (LDP) at the party's headquarters.
She told the Kyodo news agency: "I received the impression that they will not accept China's continued oppression of the Uighurs."
She has used her visit to make some highly contentious claims about the violence.
The tour with its attendant publicity has angered China
At a news conference, speaking through a translator, she said that "nearly 10,000 people" had disappeared in one night in the city of Urumqi, the capital of the Xinjiang region.
"If they are dead, where are their bodies? If they are detained, where are they?"
The BBC's China analyst, Shirong Chen, says that if the translation is correct, the figure is a political bombshell.
China's official media says about 1,700 Uighurs have been arrested - more than 1,400 suspects were detained following the riots and 253 since then.
Mrs Kadeer said China's policies towards ethnic minorities had failed and that "the only way to resolve the problem is for the World Uighur Congress and Chinese authorities to hold dialogue".
"I want China to respond to this and international society to encourage it to do so," she said.
Japan earlier insisted it had not invited Mrs Kadeer and that no officials would meet her.
It said it did not expect Mrs Kadeer's visit to affect its relations with China.
A spokesman said she was invited by civil society organisations rather than the government.
Although Mrs Kadeer's Japan visit will be relatively short, it will take a long time for Beijing to forgive the country for giving her a platform, our correspondent says.
Beijing has also expressed is disapproval of a planned visit by Mrs Kadeer to Australia.
She is to attend the Melbourne International Film Festival, which is screening a documentary about her life, 10 Conditions of Love, on 8 August.
Officially, China is made up of 56 nationalities
An Australian official said China had made repeated representations about Mrs Kadeer's visit, and that it had been discussed in both Canberra and Beijing.
The festival's director, Richard Moore, says a Chinese official has urged him to withdraw the film.
He told ABC radio that someone had hacked into the festival's website.
"This little Chinese flag sort of popped up and went ding-da-ding-ding-ding and there was a message on it that said basically they objected to the presence of this film.
"They were a concerned Chinese citizen and Rebiya Kadeer was a terrorist."
On arriving in Japan, Mrs Kadeer said she was coming to the country to tell people about what she described as the terrible conditions being endured by the Uighur minority in north-west China.
Many Uighurs there resent the influx of Han Chinese immigrants. They feel economic growth has bypassed them and complain of discrimination and diminished opportunities.