Lakhe Machrapov, 28, was detained upon his return home from Turkey after media reports said he was a possible suspect because he allegedly resembled pictures of the attacker made public by Turkish police.
Members of Kyrgyzstan's National Security Committee (GKNB) "transferred him to a regional bureau where he was questioned," said Rakhat Soulaimov, spokesman for the intelligence service, who added that investigators have been in touch with their Turkish counterparts.
Machrapov was later freed without any charges brought against him, local media reported citing the GKNB.
The foreign ministry in Kyrgyzstan said it was "improbable" that one of its nationals was involved but said it was "checking anyway".
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Turkish police have released pictures of the suspect who went on the rampage at the plush Reina nightclub on New Year's night, spraying some 120 bullets at terrified guests before slipping away into the night.
Of the 39 dead, 27 were foreigners, mainly from Arab countries, and emotional funerals were held for some of the victims today.
But the killer who Turkish authorities believe is a suspected jihadist from Central Asia remains on the run.
Neighbouring Kyrgyzstan has become more worried in the past few months over the growing influence of the Islamic State (IS) group in the majority Muslim country.
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