The captain reported that at flight planned optimum cruise altitude the aircraft failed to meet expected cruise performance. When the aircraft arrived at Perth a re-weigh of the payload was requested. The re-weigh showed that the payload was approximately 3500 kg more than was indicated on the loading documentation. This meant that the aircraft had been operated at weights in excess of its maximum zero fuel weight and maximum brakes release weight. The investigation revealed that four unrelated factors had contributed to the overloading of the aircraft. The first involved accepting freight from another air freight company on the basis of the weights provided by that company and not re-weighing the freight to check the weights. The second involved weighing freight on scales with which the airfreight personnel were not familiar and not properly positioning the freight trolleys on the scales. The third involved a communication breakdown between loading personnel which resulted in freight being loaded on the aircraft that was not included in the loading documentation. The final factor was minor in nature and involved last minute removal and addition of freight from/into containers without accurate adjustments being made to the loading documentation. The company has addressed these problems and taken corrective action to prevent a recurrence.