A method and system for encrypting a video compressed with MPEG-4 FGS compression with minimal overhead is provided. The encryption system encrypts the video into independently encrypted segments that can be either a video packet or a video block. When the encryption system encrypts based on video packets, it encrypts the data to ensure that the encrypted data does not emulate any video packet delimiting markers. When the encryption system encrypts based on video blocks, it encrypts the coded bitstream for each video block independently, from the most significant bitplane to the least significant bitplane, using either a stream or a block cipher. After all the video blocks are independently encrypted, the encryption system partitions the encrypted data into video packets and adds a buffering bit, if necessary, to prevent emulation of video packet delimiting markers. The encryption system may generate an initialization vector for each independently encrypted segment.