The member countries also agreed to transfer at the same time the London-based Martime Security Centre Horn of Africa, which informs shipping about piracy threats off Somalia, to the French port of Brest, an EU statement said.
The security centre will remain under the Atalanta command.
The EU launched Atalanta in 2008 to fight brazen acts of piracy off the coast of Somalia, including the spectacular hijacking of a Spanish tuna boat in 2009.
Although the pirates released the crew after receiving a ransom, two of them were detained days later by European military officers.
EU countries “decided to relocate the European Union Naval Force (EU NAVFOR) Operational Headquarters from Northwood (UK) to Rota (Spain), and to Brest (France) for the Maritime Security Centre Horn of Africa (MSCHOA) as of 29 March 2019,” an EU statement said.
The member countries also decided to replace Atalanta's operational commander Major General Charlie Stickland with Vice Admiral Anotnio Martorell Lacave, a Spanish navy commander.
“During this time ATALANTA will be conducting business as usual with the Force Headquarters and ships remaining deployed and conducting deterrence of piracy and protection of WFP shipping,” Strickland said in a separate statement.
Italian, German and Spanish navy ships currently patrol the waters near Somalia, ensuring in particular the safe delivery of aid from the World Food Programme to Somalia.
EU member states on Monday also extended by one year the mandate of Operation Atalanta until December 31, 2020, they said in a statement.
The number of attacks off the coast of Somalia in the Indian Ocean has fallen from a peak of 176 in 2011 to seven in 2017 and only one has been recorded since the beginning of 2018.