The Westminster and two other naval ships, departed Aug. 12 from Portsmouth and are ultimately bound for the Persian Gulf region for military exercises.
A crowd of locals living in Gibraltar gathered at the quayside, waving British flags, Britain's The Telegraph reported.
"I feel very emotional, very patriotic," local Andrea Jones said. "It means a lot to us Gibraltarians to have naval ships here during these troubled times."
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.
Jose Manuel Barroso, the president of the European Union Commission told Spanish Prime Minister Mariano Rajoy Monday that it's illegal for Spain to impose a fee for crossing the Gibraltar border, The Telegraph reported.
Barroso asked Spain to "respect the law of the European Union.
"The commission hopes that these two member states hold dialogue as members of the European Union. It also falls to them to find a solution and overcome obstacles," said EU spokesman Olivier Bailly.