The pilot of VH-MVX was given a departure instruction to turn left onto a heading of 030 degrees and to maintain 2,000 ft. The departure was being made from runway 15. The pilot had planned to cruise at 9,000 ft. The restriction to 2,000 ft was due to an inbound jet on the 153 radial which had been assigned 3,000 ft, and had been programmed for a left circuit for runway 15. VH-MVX was cleared for takeoff, and before the pilot contacted the departures frequency, the departures controller advised the tower that the jet would be now tracking for a right circuit. After sighting the inbound jet, the tower controller volunteered to separate the two aircraft. On first contact with the departures controller, the pilot of VH-MVX reported on climb to 9,000 ft, the flight planned altitude. Since the separation problem had been resolved, the departures controller thought that the tower had cancelled the altitude restriction and he accepted the altitude without comment. The pilot of VH-MVX subsequently reported maintaining 3,000 ft. There was no restriction by this stage and the pilot was cleared to climb to 9,000 ft. For this sector, the captain was the pilot flying (PF), and the copilot was the pilot not flying (PNF). The clearance instructions and restrictions were correctly received, understood, and readback by the crew. The assigned altitude 2,000 was placed in the assigned altitude indicator. This is to remind the crew of the last assigned altiude. After takeoff, the PNF contacted departures in the normal manner. He reported climbing to the originally cleared and planned level of 9,000 ft. This incorrect level advice was not challenged by the approach controller. The PNF could not explain why he forgot the 2,000 ft restriction. The captain stated that he did not hear the copilot say 9,000, believing he said 2,000. The departure controller then requested the pilot accept amended tracking instructions. These were accepted, again without reference to the 2,000 ft restriction. Company Standard Operating Procedures (SOP's) require the PNF to refer to the assigned altitude indicator when reading back altitude clearances issued by air traffic control. The captain stated that he was happy to comply with the amended tracking instructions, was well aware of the restriction to 2,000 and was intending to comply with this restriction as well. He then subsequently climbed through the restricted altitude. Company SOP's require the PF to initiate altitude calls at 1,000 ft and 500 ft to go to assigned levels and for the PNF to respond. These calls were not made, nor challenged. The occurrence was allowed to develop through the failure of air traffic control and the crew to maintain adequate situational awareness. The safety net failed when the crew failed to comply with SOP's, cockpit management was inadequate, and the copilots support role was also inadequate. Action has been taken by the company to improve crew performance, and a notice issued to all pilots instructing them to apply extra vigilance to their duties.