Ms Kadeer is travelling to Japan to attend the World Uyghur Congress's general assembly.
Her arrival will coincide with Japanese Prime Minister Yoshihiko Noda's attendance at a trilateral meeting with Chinese Premier Wen Jiabao and South Korean President Lee Myung Bak, in Beijing.
China has called on Japan and other countries not to support Ms Kadeer's "anti-China separatist activities".
Her entry to Japan may irritate Beijing, which reportedly asked Tokyo to refrain from issuing an entry visa.
"Based on Japan's law, we just carried out the (visa) issuance procedure," a senior Japanese Government official told Kyodo news agency.
The Uyghur people are an ethnic minority from the northwest region of Xinjiang province who are mainly Muslim.
Ms Kadeer was one of China's wealthiest entrepreneurs before her work advocating for the rights and self-determination of the Uyghur people put her in conflict with the Chinese Government.
In 2000 she was jailed for "endangering state secrets", reportedly because she sent newspaper articles to her husband in the United States.
After her release from prison in 2005 Ms Kadeer fled to the US.
Ms Kadeer made headlines around the world in 2009 when the Chinese Government asked the Melbourne International Film Festival to withdraw a documentary about her.
At the time China was accusing Ms Kadeer of being involved in organising riots which had the month before killed more than 180 people. Ms Kadeer denied the allegations.