The squadron moved to RAF Akrotiri on Cyprus in August 1956 as Britain and France prepared a military response to the Egyptian Nationalisation of the Suez Canal. On 31 October, the British and French launched Operation Musketeer, a series of heavy air attacks against Egyptian targets followed by landings on 6 November. No. 39 Squadron's role was to protect the vital airfields on Cyprus from any potential Egyptian retaliation. Pressure from the UN forced a ceasefire in Egypt and a withdrawal of the Anglo-French forces by the end of December, but the squadron remained in Cyprus after the British forces dispersed, flying patrols to deter aircraft that were suspected of dropping supplies to EOKA forces fighting against the British rule of Cyprus. The main body of the squadron returned to Malta in March 1957, but a detachment was maintained on Cyprus. Tensions in Lebanon (which eventually culminated in the Lebanon Crisis of July–October 1958) caused the whole squadron to move to Cyprus in May 1958, but it soon returned to Malta and disbanded on 30 June 1958.