The Boeing-737 bound for Tehran crashed on August 24 soon after takeoff. All seven crewmembers and only 18 of the 83 passengers on board survived.
The 24.kg news agency said the 54-year-old pilot, Yury Goncharov, is currently in custody at a detention center and is expected to be charged with breaching safety regulations.
The plane was carrying a number of foreign nationals, mainly Iranians, as well as Kazakhs, Canadians, Chinese, and Turks. It is believed that 52 of the dead were Iranian nationals.
Initially Kyrgyz authorities said cabin decompression, a fault in the flight control system or engine failure, could have been among the possible causes of the crash.
It was reported earlier that flight information stored on the plane's black box recorders, which were recovered from the wreckage by investigators, was missing.
Kyrgyz authorities are also trying to trace two female passengers, believed to be local students, who allegedly fled the crash scene in a state of shock.
To date only 11 bodies have been officially identified.
