The militants abducted the Kyrgyz man together with eight Turkish nationals, a Russian and an Afghan interpreter on April 21 after their helicopter made a hard landing in Logar province.
Taliban spokesman Zabihullah Mujahid, speaking to AFP by phone from an unknown location, said the hostage was freed as a goodwill gesture to the Kyrgyz government.
The militants had earlier freed the Turkish nationals following the largest abduction of foreigners in Afghanistan in almost six years, highlighting the country's continuing insecurity as NATO combat troops prepare to pull out next year.
Mujahid said the Kyrgyz national was freed "as (an) Islamic and humanitarian gesture of respect to his Islamic country".
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Asked why the Afghan national had not been freed, the rebel spokesman said he was being investigated for "possible ties with intelligence agencies", but added that the rebel group would not execute him.
Turkey, one of only two Muslim-majority members of NATO, has around 1,800 soldiers serving with the US-led military coalition, but they do not take part in combat operations.