"We demand China immediately correct its mistaken methods and release Ilham Tohti," Dilxat Raxit, spokesman for the World Uyghur Congress (WUC) said in an e-mail.
Raxit said that China's accusation against Tohti was a "complete political decision" that was not in accordance with the law.
Prosecutors in the far western Xinjiang region yesterday announced they were charging Tohti with separatism following his detention earlier this year, sparking renewed international calls for his release.
Tohti, who taught at a university in Beijing, has been a vocal critic of the government's policies toward his mostly Muslim Uighur minority, who are concentrated in Xinjiang.
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The United States yesterday called on China to free Tohti, saying it was "concerned" over reports of his indictment.
But in a sharp riposte Beijing today urged Washington to not interfere in its affairs.
"The US side has on many occasions made irresponsible remarks on China's law enforcement and judicial practices under the disguise of their so-called 'human rights' and 'freedom' which constitutes wanton interference in China's sovereignty," said foreign ministry spokesman Qin Gang.
But the Human Rights Watch (HRW) called the charges against Tohti "deeply disturbing".
"The decision to indict on such a serious charge a man like Ilham Tohti, who is known for trying to bridge divides, shows how far China's human rights have deteriorated in the past months," Sophie Richardson, HRW's China director, said in a statement today.
"It sends precisely the wrong signal to Uighurs when tensions are at an all-time high."
The charges come as China is cracking down over a series of violent attacks that blames on religious extremists and "terrorists" seeking independence for the region.
China blames militants from Xinjiang for an attack in Urumqi that killed 31 people in May, and for a March stabbing spree at a train station in the southwestern city of Kunming in which 29 people died.
Rights groups and many analysts and academics counter that the cause of the unrest can be found in state cultural and religious repression of Uighurs.