Methods and systems for controlling a physical system (plant) are disclosed. The plant is modeled as a linear, finite-dimensional system having a state vector, a control input vector, a plant output vector, and a disturbance vector comprising disturbances having known basis functions and unknown amplitudes. An adaptive control law is used with separate adaptive gains for an error vector associated with the plant output vector, and the disturbance vector, plus a fixed gain for a disturbance estimator. The adaptive control law is operable to adjust the control input vector so as to minimize the error vector. The plant includes modes which are not Almost Strictly Positive Real (ASPR).