Linear LQG controller has been investigated to control flexible link manipulators. The performance and complexity of these depend largely on the model upon which the controller is designed. In this study, the flexible modes of the link manipulator are considered to have uncertain parameters, which can be represented by random variable and these parameters are reflected on the weighting of performance. In this method, the exact modelling for the flexible modes is not necessary. The order of the resulting controller is much lower than the one based on a full model. Through numerical study, it is shown that the performance and the stability-robustness of the proposed controller reaches reasonably the one based on the full model.