While VH-CZE was lining up a helicopter was cleared for takeoff from the southern end of the parking areas to the west of the runway. The helicopter was instructed to remain west of the flight strip and to cruise not above 500 ft. The helicopter pilot maintained the runway heading for about one mile past the end of the runway before slowly moving left to track around the coast to his destination adjacent to the Cairns city area. When he started to move left VH-CZE was in the latter stages of the takeoff. As the crew had expected the helicopter to remain west of the centreline and it had now drifted into their path, they abandoned the takeoff. The helicopter was maintaining 400 ft at that time. The tower controller intended that the helicopter should remain west of the runway until he instructed otherwise. The helicopter pilot was new to the area and did not fully understand the intent of the instruction.