This research work provides the development of an Adaptive Flight Control System (AFCS) for autonomous hover of a Rotary-wing Unmanned Aerial Vehicle (RUAV). Due to the complex, nonlinear and time-varying dynamics of the RUAV, indirect adaptive control using the Model Predictive Control (MPC) is utilised. The performance of the MPC mainly depends on the model of the RUAV used for predicting the future behaviour. Due to the complexities associated with the RUAV dynamics, a neural network based black box identification technique is used for modelling the behaviour of the RUAV. Auto-regressive neural network architecture is developed for offline and online modelling purposes. A hybrid modelling technique that exploits the advantages of both the offline and the online models is proposed. In the hybrid modelling technique, the predictions from the offline trained model are corrected by using the error predictions from the online model at every sample time. To reduce the computational time for training the neural networks, a principal component analysis based algorithm that reduces the dimension of the input training data is also proposed. This approach is shown to reduce the computational time significantly. These identification techniques are validated in numerical simulations before flight testing in the Eagle and RMAX helicopter platforms. Using the successfully validated models of the RUAVs, Neural Network based Model Predictive Controller (NN-MPC) is developed taking into account the non-linearity of the RUAVs and constraints into consideration. The parameters of the MPC are chosen to satisfy the performance requirements imposed on the flight controller. The optimisation problem is solved numerically using nonlinear optimisation techniques. The performance of the controller is extensively validated using numerical simulation models before flight testing. The effects of actuator and sensor delays and noises along with the wind gusts are taken into account during these numerical simulations. In addition, the robustness of the controller is validated numerically for possible parameter variations. The numerical simulation results are compared with a base-line PID controller. Finally, the NN-MPCs are flight tested for height control and autonomous hover. For these, SISO as well as multiple SISO controllers are used. The flight tests are conducted in varying weather conditions to validate the utility of the control technique. The NN-MPC in conjunction with the proposed hybrid modelling technique is shown to handle additional disturbances successfully. Extensive flight test results provide justification for the use of the NN-MPC technique as a reliable technique for control of non-linear complex dynamic systems such as RUAVs.