Recent advances in minimally invasive surgery (MIS) have allowed patients to benefit from reduced trauma, faster recover times, and shorter hospitalisation. As a result, surgeons operate in a less-than-comfortable posture which is both physically and mentally challenging. This has led to a more demanding training scheme to acquire the relevant surgical skills. Navigating and operating with flexible instruments such as endoscopes can also induce spatial disorientation within the surgeon, where such instances are associated with increased pain for the patient and more critically, risk of perforating delicate patient tissue. Furthermore, the increased physical separation between the surgeon and the operative site and newly introduced surgical instruments have significantly changed the ergonomics and surgical workflow, which in turn increases the cognitive burden on the surgeon. The perceptual and ergonomic challenges during flexible endoscope based MIS are investigated through using the wealth of perceptual information the gaze can provide. In particular, the visualisation, navigation and ergonomic issues during MIS procedures are studied. A gaze parameter based framework is introduced to assess the use of a new field-of-view expansion technique for improved visualisation and camera trajectory comprehension when disorientated. Flexible instruments such as endoscopes suffer from disorientation inducing perceptual-motor misalignment. A misalignment quantification approach and a classification method based on gaze to infer varying perceptual-motor misalignment are developed to enable ergonomic assessment during endoscopic procedures. A novel robotic assisted gaze controlled camera system is developed to improve camera navigation where the user's control intentions are conveyed to the robotic laparoscope via real-time gaze gestures. To further improve the ergonomics of the gaze contingent system, an online calibration algorithm is integrated into the system. Throughout the thesis, detailed validation and discussion of the results are conducted to demonstrate the potential clinical value of the work.