The order for suspension of the Air Operator Permit (AOP) or flying licence of Air Pegasus was issued on November 8, 2016, according to the DGCA.
Air Pegasus has not been operating its services since July 27 following huge losses and its failure to pay lease rentals to the aircraft lessors.
Earlier on October 5, the Directorate General of Civil Aviation (DGCA) had issued a show cause notice to Air Pegasus, asking why its AOP should not be suspended for its failure to carry out operations.
The regulator had given 15 days time to the regional carrier to respond to its notice.
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Before suspending operations for an indefinite period, the carrier flew from Bengaluru to at least seven destinations in southern India.
"Capability to operate services is one of the conditions to secure flying permit. However, all three aircraft of Air Pegasus are grounded and its capability (to run the services) has degraded," the official said.
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