Prior to the Second World War, the lake at Koggala was used for seaplanes. After the outbreak of war, a water runway was demarcated and a flying boat base was established, it was the largest flying-boat base in the east. The RAF flew Consolidated PBY Catalinas and Short Sunderlands of No 202 Squadron RAF, No 204 Squadron RAF, No 205 Squadron RAF, and No 230 Squadron from here. It was a Catalina from Koggala which located the fleet of Admiral Chuichi Nagumo on 4 April 1942. It was two Sunderlands from here that rescued a group of wounded Chindits from Burma in June 1944.
After the Japanese occupied the Malay Peninsula in 1942, the QEA/Imperial Airways flight from London to Sydney lost Singapore, its refueling point between Calcutta and Perth, Western Australia. It was vital to the British/Australian war effort that the flight be maintained at any cost, so an alternate route was established through Koggala.
QEA and Imperial Airways flew Consolidated PBY Catalina flying boats from Koggala lake to the Swan River at Perth, on what was at the time the world's longest non-stop air route. The aeroplanes each carried three passengers, and 60 kg (132.3 lb) of mail. At 28 hours, the flight was so long that the passengers saw the sun rise twice, and it came to be called the 'flight of The Double Sunrise'. The first flight arrived from Perth on 30 March 1943, the last fight was on 18 July 1945. The Catalinas were replaced by civilianised Consolidated B-24 Liberator and Avro Lancastrian aeroplanes.
Meanwhile, the tarmac surface of the land runway was developed. After the war, Air Ceylon operated services to and from Koggala by Douglas DC-3 Dakota aeroplanes. In 1964, the Dakotas were replaced by Avro 748 and Nord Aviation 262 aircraft. These services were terminated following the closure of Air Ceylon in 1978.
Koggala continued as a Sri Lanka Air Force base.
The Government of Sri Lanka expects to upgrade the Koggala airport to international standards as an alternative airport to the BIA. The feasibility study, by a U.S. agency, has been completed.