The Ministry will also issue show cause notice to the operator of the chartered jet plane, Civil Aviation Secretary R N Choubey said today.
"We are going to file FIR (against the pilot) and we are also going to issue show cause notice to the operator who has flown this aircraft," Choubey told reporter on the sidelines of an aviation event here.
"And he (the pilot) is not supposed to aid anything illegal," he added.
Earlier this week, a Bihar-based businessman, travelling alone in a chartered jet, was apprehended at the Dimapur airport for allegedly carrying Rs 3.5 crore in demonetised currency.
The case was later handed over to local Income Tax authorities. They said the man had come in Dimapur on a jet that had taken off from Hissar in Haryana early on Tuesday.