The pilot of VH-CJR was conducting a flight from Prosperpine to Gladstone via Rockhampton. After passing over Charon Point he decided to track to the west of his planned track and overfly Marlborough enroute to Rockhampton and thus remain well clear of the restricted area to the east. The pilot did not advise Rockhampton Air Traffic Control of his revised tracking details. When the aircraft was 36 kilometres north-west of Rockhampton, the pilot contacted Rockhampton Tower and requested a clearance to cross the Rockhampton Contol Zone. The tower controller cleared the aircraft to track to Rockhampton remaining at least two kilometres to the east of the Rockhampton to Marlborough railway line, at an altitude of two thousand feet. The controller did not advise the pilot that the clearance was an amendment to his planned tracking details, as is required. However, the pilot acknowledged the clearance without query. This clearance was given to VH-CJR to provide lateral separation with VH-TJJ, which was about to depart Rockhampton. The pilot of VH-TJJ subsequently reported that the aircraft had departed and passed through 3000 feet. Some two and a half minutes later the pilot of VH-CJR reported the position of the aircraft as five kilometres north-west of Rockhampton at 2000 feet. Neither pilot reported sighting the other aircraft. The pilot of VH-CJR, who was inexperienced in the Rockhampton area, did not comply with the terms of his clearance.
