There is a delay of up to 40 seconds between the moment an RAF pilot sitting in Lincolnshire presses the button to release a Reaper's Hellfire missile and its impact on the ground in Helmand 4,500 miles away.

During that flight, the rocket is steered towards its target by a weapons officer sitting alongside him in an air-conditioned cabin observing a bank of video screens at RAF Waddington.

For the first time since the RAF's XIII Squadron began controlling drones – or Remotely Piloted Air Systems (RPAS) as the service prefers to describe them – over Afghanistan in April, the Ministry of Defence on Tuesday opened up its high tech operations centre.

Two squat, khaki green portable cabins stand behind a wire mesh fence inside a vast aircraft hangar. Each houses a three-person crew. Inside, they are linked by satellite communications to an airborne Reaper and British army controllers on the ground.

"It's very immersing," explained Squadron Leader Colin Redican. "I can see pictures from the Reaper. I am in touch with ground controllers. There may be pictures coming in from another Reaper in the area."

Clocks inside the cabin are set forward four-and-a-half hours to Kabul time. "We want to remove the Taliban from the battlefield without any civilian casualties," Redican said.

"People will be making assessments. We deal with that individual when the opportunity presents itself … I guide the weapon in."

The RAF has released an aerial video of an insurgent firing at British troops from outside a village. By the time the missile neared its target, the man had fled back inside the compound; the missile was directed outside the village to explode harmlessly.

Figures released by the MoD reveal that there have been 459 strikes by British-operated Reapers in Afghanistan. Only one attack, in March 2011, which hit a pick-up trucks carrying explosives, is accepted as having caused unintended casualties: four civilians died.

The defence secretary, Philip Hammond, visited RAF Waddington on Tuesday, saying he wanted to "demystify" drones. "Any new technology," he maintained, "is bound to raise concerns. People should have no greater concern about the deployment of RPAS than they would, for example, have with a Tornado [plane]."

In the week that David Cameron declared that the mission in Afghanistan will have been accomplished next year, Hammond declined to say what would happen to the five Reapers already operated by the RAF and a further five due to arrive in the coming weeks. "We will bring them out [of Afghanistan] and locate them elsewhere," he said.

Elsewhere, the Royal Navy's new unarmed, reconnaissance ScanEagle drone, it was revealed, has been flown off a frigate on active service the first time this week. It is understood to have been used in anti-pirate operations off East Africa. But asked whether the Reapers could be redeployed in Yemen, Hammond said: "We have to pursue the terrorists whereever they take themselves … Wherever there's an ungoverned space there's a risk [of terrorist activity]."

Unmanned flights within Europe are severely limited by air traffic control regulations. By 2020, however, according to Air Vice Marshal Phil Osborn, the aim is to carry out training in unsegregated airspace. "There's no intent to do surveillance in the UK," he said, "but under the Scavenger programme, we aim to fly in general airspace by the end of the decade."

The Reapers used in Afghanistan have to take off and land under local control in Afghanistan. The 0.9 second control delay, due to long-distance routing of satellite communications, means that it would also be difficult operating a drone in aerial combat.

Corporal Chris Jones, who works at RAF Waddington, has served in Afghanistan and Iraq. "I have been on the receiving end of what the insurgents are doing and I'm at peace with [bombing them]. We follow strict rules of engagement. The guys don't release anything unless they are 100% sure … There's a common misconception that it's like a PlayStation game. It's not. It's exactly the same as flying."

RAF Waddington has been the focus of anti-drone protests. Six people, included two priests, were found guilty of causing criminal damage earlier this year after cutting the fence and breaking in.

In the ground control cabins, the crews work eight-hour shifts including through the night. Each officer usually has five hours a shift in front of the screen with regular breaks to ensure peak concentration. The daily transition from family life in Lincolnshire to flying strike missions remotely over Afghanistan and returning back home again has raised concern about the stress imposed on aircrew. Medical and spiritual support, the RAF, said, is always available – as it is in other parts of the services.

"It's constant operations for two to three years," said Redican. "Briefing and debriefing are very important …. That is how we ease the transition, from this to heading off down the A46."