A modified compressed block decomposition (CBD) preconditioner combined with the multilevel fast multipole algorithm (MLFMA) is proposed for efficiently solving large dense complex linear systems that arise in electromagnetic problems.The modified preconditioner utilizes some improvements to improve the CBD preconditioner which is constructed from the available sparse near-field matrix. On the basis of the modified preconditioner, an efficient matrix–vector multiplication is implemented. Accordingly, the modified preconditioner is comparable with the unpreconditioned generalized minimal residual algorithm (GMRES) in terms of the number of iterations and the total solution time. Remarkably, the modified preconditioner provides a reduction close to one order of magnitude in both the number of iterations and the total solution time. © 2011 Wiley Periodicals, Inc. Microwave Opt Technol Lett, 2011; View this article online at wileyonlinelibrary.com. DOI 10.1002/mop.26149