Vyacheslav Kasymov, who heads the SCO's Regional Antiterrorism Structure, which based in Tashkent, also accused Washington and Tirana of using "double standards" in their fight against terror.
The five Uyghurs were recently released from the U.S. military prison in Guantanamo Bay in which the United States keeps suspected terrorists. However, Washington sent them to Albania amid concerns that they could face persecution, or execution in China.
The five have requested political asylum in Albania.
China accuses elements of its Uyghur minority of seeking independence through violent means. Rights campaigners in turn accuse Beijing of violating the rights of Uyghurs, most of whom live in the western region of Xinjiang.
The SCO is dominated by China and Russia. The other members are Kazakhstan, Kyrgyzstan, Tajikistan, and Uzbekistan.