Vertical separation diminished to about 500 feet between two aircraft in controlled airspace. VH-STC was on climb from Essendon, and VH-TWC was ex Geelong and cruising at 6,000 feet. Initially VH-STJ was cleared to climb to 6,000 feet, but when the departures controller realised that VH-STJ's groundspeed was too slow for it to remain ahead of VH-TWC, he cleared VH-STJ on climb to 5,000 feet and wrote the amended altitude on VH-STJ's flight strip. To resolve potential conflict with other traffic in the Melbourne area, both VH-STJ and VH-TWC were issued with an amended route clearance, Melbourne - Fentons Hill - Mangalore. When issuing this amended route clearance, the controller followed the normal practice of including the cleared level. However, he inadvertently cleared VH-STJ to the original flight planned altitude of 6,000 feet instead of the amended altitude of 5,000. When the controller noticed by radar that VH-STJ continued to climb through 5,000 feet he queried the pilot who discontinued the climb. Significant Factor The following factor was considered relevant to the development of the incident: 1. The air traffic controller inadvertently cleared VH-STJ to the wrong altitude.