It is a recurrent issue in astronomical data analysis that observations are incomplete maps with missing patches or intentionally masked parts. In addition, many astrophysical emissions are nonstationary processes over the sky. All these effects impair data processing techniques which work in the Fourier domain. Spectral matching ICA (SMICA) is a source separation method based on spectral matching in Fourier space designed for the separation of diffuse astrophysical emissions in cosmic microwave background observations. This paper proposes an extension of SMICA to the wavelet domain and demonstrates the effectiveness of wavelet-based statistics for dealing with gaps in the data.