The Medipix3, a hybrid pixel detector with a silicon sensor, has been evaluated as a beam instrumentation device with proton and carbon ion measurements at EBG GmbH MedAustron IR1 (Irradiation Room 1), Marie-Curie-Straße 5, 2700 Wiener Neustadt, Austria. Protons energies are varied from 62.4 to 800 MeV with 10^4 to 10^8 protons per second impinging on the detector surface. For carbon ions, energies are varied from 120 to 400 MeV/A with 10^7 to 10^8 carbon ions per second. Measurements include simultaneous high resolution, beam profile and beam intensity with various beam parameters at up to 1000 FPS (frames per second), count rate linearity and an assessment of radiation damage after the measurement day using a X-ray tube to provide a homogeneous radiation measurement. The count rate linearity is found to be linear within the uncertainties (dominated by accelerator related sources) for the measurements without degraders. Various frequency components are identified within the beam intensity over time firstly including 49.98 Hz with standard deviation, σ = 0.29, secondly 30.55 Hz σ = 0.55 and thirdly 252.51 Hz σ = 0.83. A direct correlation between the number of zero counting and noisy pixels is observed in the measurements with the highest flux. No conclusive evidence of long term radiation damage was found as a result of these measurements over one day.