The Partenavia was being flown from Essendon to Sydney. During the final stage of the flight the aircraft was radar vectored for an approach and landing on runway 34, which was accomplished normally. After landing, the aircraft vacated left into taxiway 'Alpha' and contacted Surface Movement Control (SMC), which cleared the aircraft to cross runway 34 via taxiway 'Hotel' and hold short of runway 07. Although this was acknowledged by the pilot, the aircraft continued past the holding point on taxiway 'Charlie' and infringed the runway 07 flight strip, despite being queried by SMC. When the pilot of the Partenavia recognised the aircraft had entered the flight strip he immediately carried out a 180 degree turn to vacate, during which the runway surface itself was slightly infringed. In the meantime, a Boeing 737, VH-TJO, which had been cleared to take-off on runway 07, was instructed by the Aerodrome Controller (ADC) to stop immediately. This was accomplished safely from a reported speed of 100 knots. The aircraft was able to vacate the runway via taxiway 'Charlie'.