With the outbreak of World War II the Australia-England route, over which the flying boats operated, became a vital line of communication. Qantas pilots continued to fly to Singapore, maintaining the thrice-weekly services. Singapore fell to Japanese forces and the last Qantas flying boat escaped the beleaguered island by moonlight on 4 February 1942.
Qantas crews were in the front line, operating unarmed aircraft on dangerous missions as the enemy advanced southwards through the islands.
They hid flying boats under trees to evade enemy aircraft. They saved an Empire flying boat near a burning munition ship in Darwin Harbour, taking off moments before the 11,000 tonne 'Neptuna' exploded with such force that the stern landed the other side of the wharf.
Japanese Zeros shot down Captain Aub Koch's flying boat while he was evacuating women and children from Surabaya. Shot through the arm and leg, he swam 8km ashore. Later when another of his aircraft was lost near Port Moresby, he gave his lifebelt to a passenger and swam unaided for 19 hours. There were many similar acts of heroism.
The flying boats were recalled to Australia. By March 1942, of the 10 that had been operated by Qantas, three had been destroyed by the enemy and another two lost in accidents resulting from wartime service.
Qantas continued a Brisbane-Darwin service and a handful of minor Queensland routes, but overseas passenger services were curtailed until the end of the war. More than half the fleet was commissioned for war service by the Australian Government. Flying boats now operated between Townsville in North Queensland and Port Moresby and Milne Bay in New Guinea.
Qantas crews later served in the battle zones of New Guinea. Combined Qantas and RAAF personnel flew Empire flying boats and Lockheed Lodestars, dropping supplies to Australian troops fighting their way along the famous Kokoda Trail. A Lockheed 10 and two Qantas DH86s later joined the New Guinea supply operations.