Tohti, 44, a Beijing resident, was being held in Urumqi, the capital of Xinjiang Uighur Autonomous Region in western China, after his arrest six weeks ago in Beijing, authorities confirmed.
Tohti is an outspoken critic of Chinese policy in the energy-rich region. Tensions between native Uighurs and Chinese security forces have resulted in weekly clashes and the loss of over 100 lives in recent months, the New York Times reported Wednesday.
His formal arrest underscored the government's determination to silence a moderate voice for the Uighurs, a predominately Sunni Muslim people, the newspaper said.
Accusations of fomenting separatism are baseless, Tohti's lawyer, Li Fangping, said Wednesday.
Tohti's wife, Guzaili Nu'er, denied any separatist ambitions of her husband, saying, "He is a sensible, educated man who just studied human rights, culture and religion in Xinjiang."