RAF's unmanned Reaper aircraft had been operated from Creech airforce base in Nevada, but missions from Lincolnshire began this week

Remotely controlled armed drones used to target insurgents in Afghanistan have been operated from the UK for the first time, the Ministry of Defence said on Thursday.

Missions of the missile-carrying Reaper aircraft began from a newly built headquarters at RAF Waddington in Lincolnshire earlier this week – five years after the MoD bought the unmanned aerial vehicles (UAVs) to monitor and attack the Taliban.

Since then the UK has been controlling the RAF's five Reaper aircraft from Creech airforce base in Nevada because the British military did not have the capability to fly them from here.

However, the MoD made building a new UAV hub at Waddington a priority following the 2010 strategic defence and security review, and the centre "stood up" at the end of last year.

Waddington has become the home of XIII squadron, and defence officials said pilots from the unit have now started to take command of Reapers, working in tandem with the team in America.

There are three operating terminals at the base in Lincolnshire, and they had to go through extensive technical trials before they were deemed ready for use.

"We aren't flying any more operations than we were before, but with the time differences between the US, Afghanistan and the UK, it is now possible for pilots at Waddington to work in relay with the those in the US," said a source.

There are no current plans to disband the squadron in the US, which is expected to continue operating until the end of next year, when all Nato combat operations in Afghanistan will finally come to an end.

The RAF has bought five more Reaper aircraft, which are expected to be deployed in Afghanistan over the summer, bringing the total to 10. British UAVs have flown 45,000 hours in Afghanistan, and fired 350 weapons, including Hellfire missiles.

Though the MoD insists it operates with aircraft only in support of British troops, and only in Helmand province, the use of UAVs has been dominated by the CIA's controversial programme to target insurgent leaders in Pakistan.

These strikes have sometimes caused civilian casualties, and have raised questions over the legality and morality of using remotely piloted systems in areas that are not conflict zones.

The disclosure comes at a sensitive time for the MoD – just two days before a protest outside RAF Waddington organised by CND, the Drone Campaign Network, Stop the War and War on Want.

The coalition has warned that switching control of drones to Waddington from US bases marks an unwelcome expansion in the UK's UAV programme.

"Drones, controlled far away from conflict zones, ease politicians' decisions to launch military strikes and order extra-judicial assassinations, without democratic oversight or accountability to the public," said Rafeef Ziadah, from War on Want.

Chris Nineham, vice-chair of the Stop the War Coalition, added: "Drones are being used to continue the deeply unpopular War on Terror, with no public scrutiny. They're using them to fight wars behind our backs. These remote-controlled killing machines should be banned."