Abdugani Kamaliyev, 49, was arrested in the western Siberian city of Tyumen on Nov. 23 and deported to Uzbekistan early Wednesday, said Yelena Ryabinina, an activist at the Civic Assistance Committee, which helps refugees.
The European Court of Human Rights had sent a decision to local authorities that ordered them not to carry out Kamaliyev's extradition before a court hearing.
Prosecutors and police in Tyumen were not immediately available for comment.
Kamaliyev, who is married to a Russian national, is accused in Uzbekistan of attempting to plot a coup, membership in a banned religious group and fomenting religious hatred -- charges punishable by up to 15 years in prison, Ryabinina said
The United Nations has said the use of torture is systematic in Uzbek jails.
Russian human rights ombudsman Vladimir Lukin had also asked for a delay in the extradition.
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