The initial alignment of inertial platform for navigation system was considered. An adaptive filtering technique is developed for the system with unknown and varying sway disturbance. It is assumed that the random sway motion is the second order ARMA(Auto Regressive Moving Average) model and performed parameter identification for unknown parameters. Designed adaptive filter contain both a Kalman filter and a self-tuning filter. This filtering system can automatically adapt to varying environmental conditions. To verify the robustness of the filtering system, the computer simulation was performed with unknown and varying sway disturbance.