The revelation comes after local residents complained about increased night time helicopter activity at the Ballykelly airfield in recent weeks. The noise has been disturbing their peaceful night's sleep.
Political reaction to the news that the area is being used by troops preparing for duty in Afghanistan has been mixed - with unionists welcoming the move but Sinn Fein criticising it.
On Friday a spokesperson for the Ministry of Defence said that the activity was an essential part of combat helicopter pilot training for Afghanistan.
He said: "All the night time flights are pre-deployment validation training flights in preparation for deployment to Afghanistan. Pilots from 206 Squadron, RAF, based at Aldegrove, are involved.
"The pilots and crew are required to be fully experienced in all manoeuvres and tactics before going into theatre. Night time flying is a very important part of the preparations and many in-theatre flights have to be at night for security reasons.
"Pilots have to train using night vision goggles. They can often be seen at night flying along the River Bann, which replicates one of the major river features to be found in Helmand Province in Afghanistan."
Unionist Councillor Leslie Cubitt has welcomed the news that the Shackleton base is still being actively used.
He said: "I am very happy to learn the base is still open.
"It means there is still some employment available there. It should never have been closed in the first place. Now I just hope that this means there will be a continued army presence in the area."
Not everyone welcomed the development and Sinn Féin Councillor Paddy Butcher has called for the immediate end to low flying helicopters over Ballykelly and Magilligan.
Councillor Butcher said: "The helicopters are a cause of great disturbance for residents and families. I have heard reports that children were frightened by the noise caused and many who had thankfully never had this experience before were unnecessarily frightened. We don't need to be going back to the days of these low flights.
"The British Army is an occupying force, therefore any kind of manoeuvres being carried out will always be viewed with suspicion. If we are to believe the British Government are serious about their role in creating a stable society then they must play their part in removing this very visible image of war."