We study vortex structure in a two-band superconductor, in which one band is ballistic and quasi-two-dimensional (2D), and the other is diffusive and three-dimensional (3D). A circular cell approximation of the vortex lattice within the quasiclassical theory of superconductivity is applied to a recently developed model appropriate for such a two-band system [Tanaka et al 2006 Phys. Rev . We assume that superconductivity in the 3D diffusive band is "weak", i.e., mostly induced, as is the case in MgB2. Hybridization with the "weak" 3D diffusive band has significant and intriguing influence on the electronic structure of the "strong" 2D ballistic band. In particular, the Coulomb repulsion and the diffusivity in the "weak" band enhance suppression of the order parameter and enlargement of the vortex core by magnetic field in the "strong" band, resulting in reduced critical temperature and field. Moreover, increased diffusivity in the "weak" band can result in an upward curvature of the upper critical field near the transition temperature. A particularly interesting feature found in our model is the appearance of additional bound states at the gap edge in the "strong" ballistic band, which are absent in the single-band case. Furthermore, coupling with the "weak" diffusive band leads to reduced band gaps and van Hove singularities of energy bands of the vortex lattice in the "strong" ballistic band. We find these intriguing features for parameter values appropriate for MgB2.