The department announced the move after talks with the airline and the Civil Aviation Authority of Thailand (CAAT), Airports of Thailand (AOT), and Aeronautical Radio of Thailand (AeroThai).
Nok Air launched the Chiang Mai-Mae Hong Son route last month but failed to sell enough tickets to make it commercially viable.
The airline also claimed insufficient aircraft as its Boeing 737-800 aircraft, which skidded off the runway at Chiang Rai Airport on July 30, was still undergoing repairs.
The department said CAAT will hold a meeting on business plans with Nok Air, AOT and AeroThai on Tuesday (November 22).
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