A method for controlling a vapour compression system (1) is disclosed. A mass flow of refrigerant along a part of the refrigerant path is estimated, based on measurements performed by one or more pressure sensors (10, 12, 13) for measuring a refrigerant pressure at selected positions along the refrigerant path and one or more temperature sensors (11, 14) for measuring a refrigerant temperature at selected positions along the refrigerant path. A refrigerant pressure or a refrigerant temperature at a selected position a pressure sensor (10, 12, 13) or temperature sensor (11, 14) along the refrigerant path is derived, based on the estimated mass flow. The vapour compression system (1) is allowed to continue operating, even if a sensor (10, 11, 12, 13, 14) is malfunctioning or unreliable.