Reference ionization chamber dosimetry implemented in a clinical proton beam and based on the ICRU 59 recommendations has been verified with an independent carbon activation method. The 12C(p,pn)11C nuclear reaction was used to measure the beam fluence and entrance dose. A method to transfer from the entrance dose to the dose at the ion chamber calibration position has been developed. Measurements performed in a monochromatic 200 MeV beam show that the ratio of absolute doses measured using the carbon activation and the ion chamber methods is 1.017 +/- 0.03 (type A uncertainty). This result is within the uncertainties of both methods employed, which are estimated at +/- 4.3% (carbon activation) and +/- 2.7% (ion chamber calibration).