This paper suggests the improvement of security in Micro Aerial Vehicle (MAV) communication protocol for the communication between the Ground Control Station (GCS) and the MAV. Proposed method involves the implementation of the Caesar Cipher method of data encryption with a secured key. The method of Ciphering is used for authentication of the Micro Aerial Vehicle at the beginning of the communication. Later the same is used for critical command, control and parameter messages at varied frequencies. This results in improvement of security and reliability of the system in defense and other high security applications.