The pilot of VH-NPD, operating IFR and tracking from Port Augusta to Adelaide at 7,000ft, requested Adelaide Flight Service for a change of altitude to 9,000ft. Adelaide Flight Service arranged the altitude change and advised there was no other IFR traffic in the area. VH-JVN, another IFR aircraft, had been cleared direct from Adelaide to Leigh Creek at 9,000ft, and therefore not assessed by air traffic control as traffic for NPD. The flight route was later changed to via Ardrossan, which put it on a reciprocal heading to NPD. The possibility of a conflict was not recognised by the sector controller before the two pilots had become concerned about the situation and arranged their own separation. The aircraft passed each other within 1km at the same altitude.