Government spokeswoman Roza Daudova said 22 of the 90 people who were on board the aircraft survived, including two crew members.
She said that 18 people had been taken to hospital while four others were sent home with no serious injuries.
An official at Manas International Airport said the crash occurred after the crew reported a technical problem on board about 10 minutes into the flight.
The Boeing 737 belonged to a private Kyrgyz company, Itek-Air, but was operated by Iran Aseman Airlines, she added.
The Interfax news agency reported that it was heading from Kyrgyzstan to Mashhad in eastern Iran.
The US base at Manas airport sent ambulances and firefighting equipment in response to a request for help, Major Damian Pickart said.
Itek Air has been banned from operating in the airspace of the European Union because of failure to meet safety and aviation standards, according to a list published by the EU on July 24.
Kyrgyzstan is a poor, mountainous country west of China.
The US airbase in the country supports operations in nearby Afghanistan.