A method for handling bodily waste including medical substances, such as antibiotics, present in dissolved state in the bodily waste, said method comprising: in at least one buffer tank, receiving an aqueous composition containing medical substances present in dissolved state in bodily waste; temporarily storing the aqueous composition in the buffer tank; transferring the aqueous composition in batches from the buffer tank to a vaporization unit comprising one or more vaporization chambers (26, 28); in said one or more vaporization chambers (26, 28), vaporizing water from the aqueous composition for producing a water-reduced waste material containing said medical substances, wherein, the water content of the aqueous composition is reduced in the vaporization unit by 30-95%; passing the vaporized water through one or more protective structures (59, 79), such as one or more demisters, arranged to prevent aerosols or droplets to pass through; transferring the waste material from the vaporization unit to a plurality of waste containers; vaporizing additional water from the waste material in said waste containers by heating and/or pressure reduction, for producing a further water-reduced waste material; removing and replacing said one or more waste containers containing said waste material; and subjecting removed waste containers together with the waste material contained therein to a destructive treatment, such as a high-temperature incineration process; wherein the waste material is transferred from the vaporization unit into said plurality of waste containers in sequence such that while one or more waste containers are being filled, water is being vaporized, by heating and/or pressure reduction, from waste material present in one or more previously filled waste containers. in at least one buffer tank, receiving an aqueous composition containing medical substances present in dissolved state in bodily waste; temporarily storing the aqueous composition in the buffer tank; transferring the aqueous composition in batches from the buffer tank to a vaporization unit comprising one or more vaporization chambers (26, 28); in said one or more vaporization chambers (26, 28), vaporizing water from the aqueous composition for producing a water-reduced waste material containing said medical substances, wherein, the water content of the aqueous composition is reduced in the vaporization unit by 30-95%; passing the vaporized water through one or more protective structures (59, 79), such as one or more demisters, arranged to prevent aerosols or droplets to pass through; transferring the waste material from the vaporization unit to a plurality of waste containers; vaporizing additional water from the waste material in said waste containers by heating and/or pressure reduction, for producing a further water-reduced waste material; removing and replacing said one or more waste containers containing said waste material; and subjecting removed waste containers together with the waste material contained therein to a destructive treatment, such as a high-temperature incineration process; wherein the waste material is transferred from the vaporization unit into said plurality of waste containers in sequence such that while one or more waste containers are being filled, water is being vaporized, by heating and/or pressure reduction, from waste material present in one or more previously filled waste containers.