Decentralized filtering for a formation flight instrumentation system by INS/GPS integration is considered in this paper. An elaborate tuning method of the measurement noise covariance is suggested to compensate modeling errors caused by decentralizing the extended Kalman filter. It does not require large data transfer between formation vehicles. Covariance analysis exhibits the superior performance of the proposed approach when compared with the existent decentralized filter and the global filter, which has the target-filter performance.