The patrol boat, the "7 de Agosto", joined Operation Atalanta on Saturday after undergoing combat certification by the Spanish navy in the Bay of Cadiz in southern Spain, the ministry said in a statement yesterday.
"The experience will serve as a model for the future integration of other navies," it added.
Spain in May took over the rotating helm of Operation Atalanta, which was launched by the EU in December 2008 to protect World Food Programme vessels delivering food aid to displaced people in Somalia, as well as to combat piracy off the Somali coast.
Last year Ukraine contributed a warship while New Zealand sent a maritime patrol and reconnaissance aircraft to the force.
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A Spanish navy liaison team will be on board the Colombian navy patrol boat, which has a crew of 65 people, to help coordinate day to day operations.
Pirates operating from the Somali coast have raked in millions of dollars in ransoms from hijacking ships.
At the height of Somali piracy in January 2011, 736 hostages and 32 ships were being held by pirates, according to the EU's External Action Service.