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In 1912, Paine was appointed as the first commandant of the Central Flying School, Upavon.
Three years later in 1915, after the Royal Naval Air Service has broken away from the Royal Flying Corps, the Royal Navy established the Central Depot and Training Establishment. The new unit was based at Cranwell and Paine was raised to the rank of Commodore and sent there as its first commander.
Just over a year later, in early 1917, Paine was appointed Fifth Sea Lord and Director of Naval Aviation.
With the establishment of the RAF in 1918, Paine was promoted to major-general (a rank of the RAF at that time) and sat on the Air Council as Master-General of Personnel. With the introduction of RAF-specific ranks in 1919, Paine was regraded to air vice-marshal. His last military appointment was as Inspector-General of the RAF.
On his retirement from the RAF in 12 May 1920, Paine reverted to the equivalent naval rank (rear admiral). Excluding those with honorary ranks such as royalty, Paine is possibly the only person to have held flag, general and air officer ranks.