Aircraft carrier HMS Illustrious, frigate HMS Westminster and one other, unidentified ship, departed from Portsmouth for the Mediterranean, Britain's the Daily Mail reported.
The ships, along with seven other vessels, are bound for the Persian Gulf region where they will conduct military exercises, the BBC reported.
The Ministry of Defense said the deployment was long-planned, which Spain's foreign ministry confirmed, but the docking at Gibraltar could be seen as a provocation to Spain.
Britain and Spain are in the midst of a territorial dispute over Gibraltar, a 2.6-square-mile promontory off southern Spain under British rule since 1713.
The current row began with a dispute about fishing when Spain objected to the construction of a breakwater. Britain said the structure is needed to restore fish stocks depleted by Spanish fishermen.
In recent weeks, Spain has imposed border controls for vehicles entering and leaving Gibraltar, including a $66 toll.
The British government is investigating whether the border control checks break laws on the right to free movement in the European Union, the Daily Mail reported.
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