We develop a hybrid quantum mechanical/molecular mechanical-configuration interaction (QM/MM-CI) method for calculating the absorption maxima of photoreceptor proteins such as bacteriorhodopsin. A unique point of our method, discriminating it from usual QM/MM methods, is that the ground-state electronic structure of the whole protein is first evaluated by a linear scaling-molecular orbital calculation. The resultant electronic distribution is utilized to construct a modified Fock matrix for subsequent CI calculation. In the excitation energy calculation, only the chromophore located at the photoactive center of a protein is treated quantum mechanically and the surrounding environment is approximated by classical electrostatics. Another feature of the method is that the classical region is instantaneously polarized in response to the excitation of the chromophore. This corresponds to the incorporation of electronic polarization effects of the protein part. To allow the polarization of amino acid residues, each bond of them is approximated by a cylindrical dielectric with a given polarizability. The polarization in the classical part is determined self-consistently. Here, the above method is applied to the wild type of bacteriorhodopsin (bR(568)) and its mutants. It is revealed that their absorption maxima are not reproduced without taking into account the effect of electronic polarization of the protein part. In particular, the polarization of Trp86, Trp182, and Tyr185 plays a predominant role in causing a bathochromic shift in the absorption band of bR(568).