Ilham Tohti, an economics lecturer at a university in Beijing, has been formally accused of the offence, his wife Guzaili Nu'er told AFP.
Tohti has been one of the most prominent critics of Chinese policy in Xinjiang, the vast western region where most Uighurs live and which is periodically hit by violent clashes between locals and China's security forces.
China maintains that unrest in the region is caused by terrorist groups seeking an independent state, an account denied by Uighur rights groups who complain of widespread religious repression and economic discrimination.
"We call on the international community to monitor China and free this Uighur scholar," he added in a statement.
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The US-based Uyghur Human Rights Project said in a statement the charge against Tohti "reflects not only a zero tolerance policy to Uyghur dissent, but also the growing intractability of China towards international criticism of its ethnic policies".
The group also called on China to account for the whereabouts of Tohti, who has not been allowed to contact his family or see a lawyer since his arrest last month.
Police also blamed suspects from the region for apparently deliberately crashing a car in Beijing's famous Tiananmen Square in October, killing two tourists and the three people in the vehicle.
The crash led President Xi Jinping to call for a security push in Xinjiang. Tohti had challenged the government's account of the crash.
The United States and the European Union have both condemned Tohti's arrest.
China's courts are tightly controlled by the ruling Communist party, and have previously handed lengthy jail sentences to intellectuals who have spoken out against the authorities.