Chaotic filter bank schemes have been proposed in the research literature to allow for the efficient encryption of data for real-time embedded systems. Some security flaws have been found in the underlying approaches which makes such a scheme unsafe for application in real life scenarios. In this paper, we first present an improved scheme to alleviate the weaknesses of the chaotic filter bank scheme, and add enhanced security features, to form a modified chaotic filter bank (MCFB) scheme. Next, we present a reconfigurable hardware implementation of the MCFB scheme. Implementation on reconfigurable hardware speeds up the performance of MCFB scheme by mapping some of the multipliers in design to reconfigurable look-up tables, while removing many unnecessary multipliers. An optimised implementation on Xilinx Virtex-5 XC5VLX330 FPGA gave a speedup of 30% over non-optimised direct implementation. A clock frequency of 88 MHz was obtained.