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Speaking in the Turkmen capital Ashgabat, Guterres said that "policies that limit human rights only end up alienating religious and ethnic communities, who would normally have every interest in fighting extremism."
His speech came as ministers from Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan and Uzbekistan adopted a joint declaration on strengthening regional anti-terror efforts.
Guterres also thanked the countries for their "commitment to jointly addressing and defeating the scourge of terrorism".
Central Asia's secular authoritarian governments have cracked down hard on religious groups operating outside state control state amid concerns over the potential spread of religious extremism in a region closely tied to Russia and China.
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Three states -- Uzbekistan, Tajikistan and Turkmenistan -- are designated as "Countries of Particular Concern" regarding religious freedom by the US State Department.
The UN Secretary General's visit to the region began on June 8 in Kazakhstan where he attended a meeting of the Russia and China-led Shanghai Cooperation Organisation before visiting Kyrgyzstan on Sunday.