The two pilots have been taken off duty pending an inquiry into the incident, as they and GoAir's Director (Safety) have also been asked to explain this "violation" of aviation safety rules, they said.
Entry inside cockpit of passengers or anyone who is not a crew member is banned for security reasons since the 9/11 terror strike.
The sources confirmed that the incident occurred on Wednesday on flight G8-151 when two army officers, including a Lieutenant General, travelled in the cockpit for the entire duration of the journey.
Acting on a complaint by a passenger on the flight, the Directorate General of Civil Aviation (DGCA) also sought to know from the airline whether it was carrying more people than the number of seats available on an Airbus A-320 plane.
A preliminary enquiry has already been carried out into the incident, the sources said, but refused to give any details.