There were 496 incursions in 2013 and 112 in the first three months of 2014, figures disclosed by Foreign Secretary William Hague revealed.
August last year saw the most incursions: 68 Spanish vessels entered British Gibraltar waters.
A Foreign Office spokesman said: "We are confident of UK sovereignty over British Gibraltar territorial waters under international law. We make our position clear to the Spanish government whenever appropriate and we will continue to uphold British sovereignty and use a range of proportionate naval, police and diplomatic responses to incidents."
The Spanish Ambassador to the UK was summoned to the Foreign Office earlier this month after an incursion resulted in a collision with a Royal Gibraltar Police vessel.
Europe Minister David Lidington said the activities of the Spanish state research ship and its accompanying Guardia Civil vessel were "unlawful" and dangerous.
He told ambassador Federico Trillo the UK Government would take whatever action necessary to uphold British sovereignty and protect Gibraltar.
The summoning of Mr Trillo marks the fourth time the Spanish ambassador has been publicly called in to the Foreign Office in relation to Gibraltar since the current government in Madrid took office in December 2011.
The Rock has been a long-running cause of friction between London and Madrid, with Spain maintaining a long-standing challenge to Britain's sovereignty over the territory, which it has held since 1713.
Tensions flared again last summer after Gibraltarians dropped concrete blocks into their waters to create an artificial reef. The Spanish claimed the move was meant to disrupt their fishing boats.