* First two drones to be operational by end-year
* 1,000 French troops in Mali for counter-terrorism
* Mission to 'eliminate' al Qaeda in region
PARIS, Dec 19 (Reuters) - France will deploy its first U.S.-made unarmed surveillance drones to West Africa by the end of the year, Defence Minister Jean-Yves Le Drian said on Thursday, as it seeks to "eliminate all traces of al Qaeda".
France's military intervention in Mali in January exposed its shortage of surveillance drones suitable for modern warfare, forcing it to rely on the United States to provide French commanders with intelligence from drones based in neighbouring Niger.
Paris said in June it would buy 12 Reaper reconnaissance drones built by privately owned U.S. firm General Atomics to eventually replace its EADS-made Harfang drones.
"Two drones that we have bought will be operational by the end of the year in Africa, in the Sahel. That is their main mission," Le Drian told Europe 1 radio.
Niger gave permission in January for U.S. surveillance drones to be stationed on its territory to improve intelligence on al Qaeda-linked Islamist fighters in the region.
Le Drian said pockets of militants remained in Mali, whom Paris would go after. They included veteran Islamist commander Mokhtar Belmokhtar, who claimed responsibility for attacks in Niger and on Algeria's In Amenas gas plant earlier this year.
"We have led successful counter-terrorism attacks in recent days and we will continue to act to eliminate all traces of al Qaeda," he said.
"These terrorist groups come and go, regroup and then disperse, so we need to follow them closely. This will be the role of our forces in 2014. There will be 1,000 soldiers in Mali whose main mission will be counter-terrorism."
French forces killed 19 Islamist fighters during security operations in Mali's northern region of Timbuktu earlier this month.
France intervened in Mali at the start of the year as Islamist forces, who seized control of the north in the confusion following a military coup in March 2012, pushed towards the capital Bamako.
Their advance lifted Mali to the forefront of U.S. and European security concerns, with fears the Islamists would turn the country into a base for international attacks. (Reporting by John Irish and Marine Pennetier; Editing by Mark Trevelyan)