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Lascaris War Rooms.

Malta was a centre for intelligence gathering which was sent back to London & ultimately to Bletchley Park for de-cyphering in some cases. Messages were regularly intercepted from southern Europe, the Balkans & north Africa. All services had wireless telegraphy (W/T) or radio telegraphy (R/T) & the island was said to bristle with radio masts. Malta had one of the largest Special Liason Units (SLU) in the Mediterranean. This unit was passed all intercepts & sorted them out to send to London basically. The new RAF Type X cypher machine was installed on Malta. This was an improvement on the Enigma machine used by the Germans to code their messages.
Knowledge of our cracking the Enigma codes or the fact that we had 'come by' a machine itself was the most closely guarded secret of the war. Operators (mainly women) would spend hours with earphones on intercepting messages in the most inhospitable conditions in the Lascaris Bastion deep inside the walls of Valletta. The tunnels of Lascaris & St.Angelo used were originally excavated to house galley slaves in the days of the Knights of St.John some 3 centuries earlier. These tunnels were hot & wet with roof falls at times. Clothes would grow mould within a few days. In the winter rains sea boots were used. Malta's fresh water supply was underground & filtered through these limestone rocks.
Chest & Lung ailments were common amoungst the people working in these tunnels. Also tinnitus (buzzing in the ears) was common with operators listening through earphones for long periods.
It was known that Fliegerkorps X was moving from the Norway campaign to Sicily just before Operation Excess where HMS Illustrious was badly damaged. A little knowledge was a dangerous thing & the allies had to be careful not to react to every piece of de-cyphered traffic or the Germans would have suspected we had cracked their codes.
Rommell made regular despatches to Berlin from his HQ in north Africa which were intercepted & de-cyphered.

Ernli Bradford - Siege Malta 1940 - 1943. Penguin Books.

This site shows photos of the restored Lascaris War Rooms.