Conventional treatment planning in intensity‐modulated radiation therapy (IMRT) is a trial‐and‐error process that usually involves tedious tweaking of optimization parameters. Here, we present an algorithm that automates part of this process, in particular the adaptation of voxel‐based penalties within normal tissue. Thereby, the proposed algorithm explicitly considers a priori known physical limitations of photon irradiation. The efficacy of the developed algorithm is assessed during treatment planning studies comprising 16 prostate and 5 head and neck cases. We study the eradication of hot spots in the normal tissue, effects on target coverage and target conformity, as well as selected dose volume points for organs at risk. The potential of the proposed method to generate class solutions for the two indications is investigated. Run‐times of the algorithms are reported. Physically constrained voxel‐based penalty adaptation is an adequate means to automatically detect and eradicate hot‐spots during IMRT planning while maintaining target coverage and conformity. Negative effects on organs at risk are comparably small and restricted to lower doses. Using physically constrained voxel‐based penalty adaptation, it was possible to improve the generation of class solutions for both indications. Considering the reported run‐times of less than 20 s, physically constrained voxel‐based penalty adaptation has the potential to reduce the clinical workload during planning and automated treatment plan generation in the long run, facilitating adaptive radiation treatments.PACS number(s): 87.55.de