The private carriers have been asked to respond by Wednesday to the Directorate General of Civil Aviation's directive to withdraw the surcharge, Civil Aviation Minister Praful Patel said during Question Hour.
While all private carriers have imposed this surcharge for the past few weeks, state-owned airline Indian has not.
Asked whether the private airlines were charging this surcharge on sectors where there was no air traffic congestion also, Patel said these carriers had imposed the surcharge "on their entire network".
Replying to questions, Patel said DGCA expects a shortage of around 500 pilots every year due to the growth in the industry.
Presently, there are 3,000 type rated pilots in India, he said adding there are approximately 565 foreign pilots in the country working with various airlines.
To a related question, he said the DGCA does not suo motu grant or validate the commercial pilot licences of foreign pilots.
However, Patel said if airlines wish to deploy foreign pilots/instructors, such applications are considered by DGCA for validation subject to fulfilment of prescribed conditions.