The case was registered even as Kerala Chief Minister Oommen Chandy ordered a probe into the incident.
Complaints of passengers against the pilot and also her charges against passengers would be looked into, he said.
Chandy, who had described the incident as a spontaneous reaction, said he has instructed DGP K S Balasubramaniam to investigate the matter.
Around 200 passengers of an Air India Kochi bound flight from Abu Dhabi protested and some allegedly tried to enter the cockpit after the Kochi bound flight was diverted to Thiruvananthapuram due to bad visibility.
Six passengers were detained and questioned by the Central Industrial Security Force personnel when the plane landed at Kochi after about a nine hour delay and let off.
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