In linea con uno dei suoi compiti principali, nel 2006 FRONTEX ha cominciato a organizzare e coordinare operazioni congiunte alle frontiere esterne dell'Unione europea concentrandosi sulle aree ad alto rischio di immigrazione clandestina, come le Canarie, il Mediterraneo, le frontiere terrestri orientali e i principali aeroporti europei.
In accordance with one of its main tasks, FRONTEX has started in 2006 organising and co-ordinating joint operations along the external borders of the European Union with special focus on the areas exposed to high risk of illegal immigration, such as the Canary Islands, the Mediterranean, the Eastern land borders and the major European airports.