VH-TQR [DHC8] was maintaining Flight Level [FL] 200 on the CRAVEN - Port Macquarie track on a flight from Sydney to Port Macquarie. A clearance was obtained by Sydney Sector 2 from Williamtown Air Traffic Control [ATC] for VH-TQR to transit Restricted Area R594A at and on descent from FL200. The aircraft was authorised to leave control area on descent. RAAF Air Defence personnel were controlling MAPLE 32 [FA 18] and were instructed by Williamtown ATC to ensure that the aircraft would remain east of the CRAVEN - Port Macquarie track. During vectoring procedures the Air Defence Controller allowed MAPLE 32 to cross this track and come into conflict with VH-TQR. The Senior Controller observed this situation and initiated appropriate co-ordination to rectify the confliction. There was approximately two minutes delay before the exact information reached the Air Defence Controller responsible for MAPLE 32 and by the time separation was guaranteed, the aircraft had passed the point of nearest contact. On observing the potential conflict, Sydney Sector 2 instructed VH-TQR to maintain FL190 in an attempt to provide separation. The controller had observed the altitude read out of MAPLE 32 to be FL186 and knew that VH-TQR had left FL200 on descent. VH-TQR reached FL187 prior to maintaining FL190. The aircraft came within 6.3nm and 100ft of each other. As the radar separation standard is 5nm, no breakdown in separation occurred. Significant Factors 1. The Air Defence Controller did not comply with the Air Traffic Control instruction received. 2. The time taken for the Senior Controller to co-ordinate with the Air Defence Controller placed the separation standard in jeopardy.