In October Sir Alexander Ball arrived in Malta, and a year later he was appointed as Civil Commissioner.

In August 1801, the Civil Commissioner, Charles Cameron, appointed Emmanuel Vitale as Governor of commino instead of Saverio Cassar.

The British considered taking over Lampedusa as a naval base instead of Malta, but the idea was dropped as the island did not have deep harbours and was not well developed.

In 1810, Salvatore Gatt transferred the lease to Alexander Fernandez, the British Commissariat, and the latter attempted to create a large Maltese colony on the island.

Further problems arose when the plague devastated Malta in 1813–14, and on 25 September 1814, Sir Thomas Maitland withdrew British troops from Lampedusa.