This paper describes a method for solving the permutation problem of frequency-domain blind source separation (BSS). The method analyzes the mixing system information estimated with independent component analysis (ICA). When we use widely spaced sensors or increase the sampling rate, spatial aliasing may occur for high frequencies due to the possibility of multiple cycles in the sensor spacing. In such cases, the estimated information would imply multiple possibilities for a source location. This causes some difficulty when analyzing the information. We propose a new method designed to overcome this difficulty. This method first estimates the model parameters for the mixing system at low frequencies where spatial aliasing does not occur, and then refines the estimations by using data at all frequencies. This refinement leads to precise parameter estimation and therefore precise permutation alignment. Experimental results show the effectiveness of the new method.