Karnik was appointed Chief Operating Officer-designate, pending regulatory clearances, only in July this year.
While a spokesperson for the airline said Karnik left Jet for "family reasons", there have been several other high- profile exits over the past few months.
They include two CEOs Nikos Kardassis and Gary K Toomey, Chief Commercial Officer Sudheer Raghavan, Chief Financial Officer Ravishankar Gopalakrishnan and Vice President (Investor Relations) K G Vishwanath, after Jet and Abu Dhabi- based Etihad struck the deal in November last year.
"He will continue to work with Jet Airways in an advisory capacity on key strategic initiatives," she added.
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Karnik, who took over from Hameed Ali after the latter joined the airline's board, was given the task to oversee commercial and sales functions of the airline.
Karnik had earlier worked for several global airlines like North West, Continental and Delta Airlines and was also the CEO of Global Aero Logistics, one of the largest provider of private air charter service to US military and corporates.