The incident happened on Mumbai-Delhi Jet Airways flight, which made an emergency landing at Ahmedabad airport on October 30.
A ministry official today said the case against the individual has been registered under the amended Anti- Hijacking Act and is being investigated by the National Investigation Agency (NIA).
The amended Act has stringent provisions for violators.
"The case is required to be given to them... We want the case to be investigated under the provisions of the Anti- Hijacking Act," civil aviation secretary R N Choubey said.
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According to the official quoted earlier, the ministry has issued a notification authorising the NIA to carry out probe since the Act is implemented by the ministry.
Last week, the ministry issued a notification conferring powers to probe the case to an officer at NIA.
"... the central government hereby confers on Shri Vikram Khalate, Superintendent of Police, National Investigation Agency, Mumbai, the powers of arrest, investigation and prosecution exercisable by a police officer under the Code of Criminal Procedure, 1973" in relation to the case under the Anti-Hijacking Act, 2016, the notification said.
The note, allegedly placed by Mumbai-based Gujarati jeweller Birju Kishore Salla, stated that there were hijackers and a bomb in the cargo area, officials had said.