VH-TBR had been cleared to track via air route T9 from overhead Mount Hope, South Australia to overhead Narembeen, Western Australia. The aircraft had been cruising at Flight Level(FL) 350 but shortly before the incident the pilot had requested a descent to cruise at FL 290. The aircraft was recleared to decend to and cruise at FL 290 by Perth Air Traffic Control. A short time later, the Perth controller observed a radar return, from VH-TBR, on the edge of his screen. The return indicated that the aircraft was about 54 kilometres south of the cleared track and heading in a northerly direction. The controller immediately altered the course of an eastbound Boeing 727 aircraft to ensure separation between the two aircraft. It was established that the two aircraft came within 16 kilometres of each other, but at that time they were vertically separated by 2000 feet. However, during the descent made by VH-TBR, it had passed through the level of the other aircraft when both aircraft were estimated to be about horizontally separated by 32 kilometres. At this time the separation between the two aircraft did not comply with the prescribed standards. The investigation revealed that while the VH-TBR was enroute, and having just climbed to cruise at FL 350, the aircraft captain disengaged the autopilot to retrim the aircraft for level flight. When the autopilot was then re-engaged, the normal sequence was interrupted and subsequently not completed. As a result the autopilot was not re-coupled to the Inertial Navigation System(INS). This resulted in the aircraft maintaining a constant heading and under the influence of a changing wind velocity and the absence of normal enroute heading changes the aircraft diverted from the cleared track.