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An extended multilevel fast multipole algorithm (MLFMA) formulation is presented that includes magnetic surface current densities of radiating apertures and impedance relations containing modal excitation terms. The method-of-moment (MoM) solution is based on a combined field integral equation (CFIE) written in terms of mixed potential form. Aperture waveguide modal eigenvectors and Rao-Wilton-Glisson (RWG) functions for triangular patches are utilized for basis functions of the magnetic and electric surface current densities, respectively. The applicability of the method is demonstrated at the examples of a rectangular horn cluster in a finite screen and a finite circular horn cluster feeding a subreflector. Advantages and disadvantages of the MLFMA, when applied for aperture array problems, are discussed. The method is verified by available measurements and reference calculations.