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Travellers will also be able to connect to onward flights to Auckland in New Zealand from the Australian city.
Emirates will deploy the Airbus superjumbo on a daily route from its hub to Tokyo from 1 July 2012, marking the tenth year of operations between Dubai and Japan and the airline's third year of flying to Narita airport in the Japanese capital.
The announcement highlights the carrier's commitment to the Far East and Australasia, said Richard Jewsbury, senior vice president of commercial operations in the regions.
'Emirates not only offers a world-class inflight experience but a superior global network,' he added.
'The announcement of enhanced services into Melbourne and Tokyo comes as we introduce flights from Dubai to Dublin, our 29th European destination.'