Degraded electron beams, as used for intraoperative radiation therapy (IORT) or similar complicated dosimetric situations, have different characteristics compared to conventional electron therapy beams. If international dosimetry protocols are applied in a direct manner to such degraded beams, uncertainties will be introduced in the absorbed dose determination. The Monte Carlo method has been used to verify experimentally determined relative absorbed dose distributions and output factors in an IORT geometry. Monte Carlo generated dose distributions are mostly within +/-2% or +/-2 mm of measured data. The simulated output variation between the IORT cones (relative output factors) are mostly within 2% of measured values. By comparing IORT and conventional electron beam characteristics (e.g. energy spectra, angular distributions and the contributions of different system components to these quantities) limitations and uncertainties of commonly used dosimetric techniques in IORT electron fields are quantified. The intraoperative treatment field contains a larger amount of scattered electrons, which leads to a broader energy spectrum as well as a wider angular distribution of electrons at the phantom surface. The dose from the scattered electrons can contribute up to 40% of the total dose at a depth of dose maximum, compared to approximately 10% for standard beams. A study of the energy spectra at the reference depth reveals that an uncertainty of the order of 1% can be introduced if ionization chamber based dosimetry is used to determine output factors for the investigated IORT system. We recommend that relative absorbed dose distributions and output factors in IORT electron beams and for similar complicated dosimetric situations should be determined with detectors having a small energy and angular dependence (e.g. diamond detectors or p-Si diodes).