A respiratory therapy system is configured to supply breathing gases to a patient and comprises a controller configured to control the pressure of breathable gas delivered to the patient. The system can control the flow of breathable gas to the patient taking into account whether or not a breath is detected, and whether or not the patient is awake or asleep. The system is configured to: detect when the patient is inhaling and to control the flow generator to deliver breathable gas at an inspiration pressure (IPAP), detect when the patient is exhaling and to control the flow generator to deliver breathable gas at an expiration pressure (EPAP), the EPAP being lower than the IPAP, and detect when the patient is at least one of awake and/or asleep. The system is also configured to receive or generate a back-up time related variable which is compared with a time related variable of at least a portion of a breath of the patient such that the breathable gas delivered to the patient is automatically controlled at IPAP, if inspiration is not detected in accordance with the back-up time related variable. The back-up time related variable may be a rate or duration for example. The delivery of breathable gas to the patient is further controlled if inspiration is not detected in accordance with the back-up time related variable and the system detects that the patient is awake. For example, if the patient is awake, the system may not automatically switch to IPAP, even if a breath is not detected within a predetermined time.