Absolute dose measurements for Intensity Modulated Radiotherapy (IMRT) beamlets is difficult due to the lack of lateral electron equilibrium. Recently we found that the absolute dosimetry in the penumbra region of the IMRT beamlet, can suffer from significant errors (Capote et al., Med Phys 31 (2004) 2416-2422). This work has the goal to estimate the error made when measuring the Planning Target Volume's (PTV) absolute dose by a micro ion chamber (microIC) in typical IMRT treatment. The dose error comes from the assumption that the dosimetric parameters determining the absolute dose are the same as for the reference conditions. Two IMRT treatment plans for common prostate carcinoma case, derived by forward and inverse optimisation, were considered. Detailed geometrical simulation of the microIC and the dose verification set-up was performed. The Monte Carlo (MC) simulation allows us to calculate the delivered dose to water and the dose delivered to the active volume of the ion chamber. However, the measured dose in water is usually derived from chamber readings assuming reference conditions. The MC simulation provides needed correction factors for ion chamber dosimetry in non reference conditions. Dose calculations were carried out for some representative beamlets, a combination of segments and for the delivered IMRT treatments. We observe that the largest dose errors (i.e. the largest correction factors) correspond to the smaller contribution of the corresponding IMRT beamlets to the total dose delivered in the ionization chamber within PTV. The clinical impact of the calculated dose error in PTV measured dose was found to be negligible for studied IMRT treatments.