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In this paper, an extended COvariance Matching Estimation Techniques-Extend Invariance Principle (COMET-EXIP) method is proposed to estimate interferometric synthetic aperture radar or interferometric synthetic aperture sonar (InSAS) interferometric phase in the presence of large coregistration errors, even up to one pixel. First, the extended COMET-EXIP method is presented for the application of joint-pixel-model-based interferogram estimation, through choosing a novel “unstructured model” in terms of the parameters to be estimated and decoupling the interesting parameters from the uninteresting “nuisance parameters.” Then, a fast algorithm of COMET-EXIP is proposed for the interferometric phase estimation. Finally, the ambiguity problem of the COMET-EXIP method is solved without introducing performance degradation. The simulated data and real data from the trial InSAS and X-SAR are used to verify the validity of the method. The results show that the method is robust for a wide range of signal-to-noise ratio and has a good performance on both fringe preserving and noise suppressing. In addition, the same computational speed level of the proposed method as that of the pivoting mean filtering is very attractive.