Current protocols for clinical proton beam dosimetry have not implemented any chamber-dependent correction factors for absorbed dose determination. The present work initiates a Monte Carlo study of these factors with emphasis on proton fluence perturbation effects and preliminary calculations of perturbation effects from secondary electrons. The proton Monte Carlo code PTRAN was modified to allow simulation of proton transport in non-homogeneous geometries of both unmodulated and modulated beams. The dose to water derived from the dose calculated in an air cavity agrees well with results from analytical calculations assuming a displacement of the point of measurement. For unmodulated beams small differences, limited to 0.8%, could be partially attributed to proton multiple scattering. Effects of replacing water around the cavity with wall material are explained by the introduction of a water-equivalent wall thickness. For modulated beams no significant perturbation effects arise. Secondary electron spectra are calculated analytically. Preliminary electron transport calculations with EGS4 show that wall perturbations of the order of 1% could result. Perturbation effects caused by the energy transport of secondary particles from inelastic nuclear interactions have not been studied here. Inclusion of inelastic nuclear energy transfers in the cavity dose, assuming total local absorption, indicate that separate scaling of this contribution with the ratio of total inelastic nuclear cross sections could be important.