The girl was passing through check-in with her mother on her way to Boston via Frankfurt in a Lufthansa flight.
Airport police have detained the employees, identified as Ahmed Reza and Binoy Sanyasi, on molestation charges.
The duo were caught by the mother of a nine-year-old passenger for allegedly 'touching her inappropriately' at the check-in point near the X-ray machine of the airport.
The incident took place at around 1:45 am on Monday, Mar 1.
The woman immediately registered a complaint with the airport police before going on to take the flight.
The lady and her two children went on to board the Lufthansa flight to Frankfurt after registering the complaint.
Airport sources have condemned the incident and said the both have been booked under outraging the modesty of a woman and under the Child act.