The aircraft was cleared for a visual approach to the duty runway (RWY) 11 and joined a 7km final from a right base position. The crew were advised by ATS of several military fighter aircraft taking off from RWY 29. The captain advised ATS of his position and that a traffic confliction was about to occur as he saw two of the six fighter aircraft pass above and to the left of his aircraft. The last of the section of fighters passed within 1,000 metres of the aircraft at the same level. Subsequent investigation revealed that a request for the use of a non-duty runway (RWY29) had been agreed to previously for the military aircraft, but there had been a delay with their departure. The radar controller failed to note that a non-duty runway was marked on the flight strips. Reflected radar returns were being experienced on the Surface Movement Radar and the controller misidentified these reflected returns as those of the military aircraft, and being relatively inexperienced cleared the military aircraft to take off in confliction with the approaching aircraft.