VH-KPY had been cleared to operate on a photographic survey near Perth. VH-HYI was inbound to Perth from the south-east and was tracking via a five nautical mile final for runway 03 when the radar return indicated that the aircraft were approaching the minimum separation standard. The duty Air Traffic Controller recognised the situation and gave avoidance instructions, however they were too late to prevent separation between the aircraft reducing to less than the minimum standard of five nautical miles. The Air Traffic Controller had poorly planned the arrival of VH-HYI and had allowed himself to become annoyed at a separate co-ordination problem that he had partially created. The annoyance contributed to the reduction in separation standards in as much as it reduced his concentration on the task of maintaining separation between the two aircraft whose closing speed was of the order of 500 knots.