The FIR and a list of the accused were submitted to the CBI court in a sealed envelope.
Airport Director-in charge, Muhammed Sahid told PTI that all the passengers and crew on board the flight IX 393 are safe.
The biggest investigating agency in the country is helpless when it comes to registration of cases in Kerala.
A team of experts from the Aircraft Accident Investigation Bureau (AAIB), which is investigating the accident, had inspected the site two months ago.
They allegedly took out gold that was concealed in the Karipur airport washroom and handed it over to two other members of the gang.
This has come as a solace for the family since the tragedy, the co-pilot's father Tulsi Ram Sharma said.
The injured officials, Najeeb and Albert, have been admitted to a hospital.
Eighteen people, including the pilot and co-pilot, were killed and several others injured when the flight from Dubai with 190 people on board overshot the tabletop runway and fell into a valley.
At least 18 people, including two pilots, were killed and several injured after the Air India Express aircraft coming from Dubai crashed on August 7.
The FOQA is the process of obtaining and analysing all kinds of data from flights to improve the safety and efficiency of future flight operations.