An optical phase tracking technique for an extrinsic Fabry-Perot interferometer (EFPI) is proposed in order to overcome interferometric non-linearity. Basic idea is utilizing strain-rate information, which cannot be easily obtained from an EFPI sensor itself. The proposed phase tracking system consists of a patch-type EFPI sensor and a simple on-line phase tracking logic. The patch-type EFPI sensor comprises an EFPI and a piezoelectric patch. An EFPI sensor itself has non-linear behavior due to the interferometric characteristics, and a piezoelectric material has hysteresis. However, the composed patch-type EFPI sensor system overcomes the problems that can arise when they are used individually. The dynamic characteristics of the proposed phase tracking system were investigated, and then the patch-type EFPI sensor system was applied to the active suppression of flutter, dynamic aeroelastic instability, of a swept-back composite plate structure. The proposed system has effectively reduced the amplitude of the flutter mode, and increased flutter speed.