The firm has been piecing together the staff and software needed to control the two vast floating fortresses, and on Thursday a team of 60 personnel ran through the final day of a two-week dry-run of the new integrated system.

Deep inside the company's high-security Maritime Integrated Support Centre on Portsdown Hill, a team looked out over a computer-generated model of the sea and flight deck which was broadcast on to a 2m x 9m 180 degree cinema screen, representing the view from FLYCO – the six-sided island situated on the top deck of the carrier.

The tests of the systems, part of an overall £275m deal to set up the equipment on each of the ships, will determine the layout and staffing level of the ships' core battle stations.

'We can run it as a steady-state, peacetime scenario, and then really throw a lot at them suddenly,' said Steve Dowdell, the mission system director for BAE's Integrated Systems Technology division.

'One of those we simulated was a crash on deck – we had aircraft coming in which couldn't use the landing space they wanted to, and there's an accident.

'That's the kind of thing that can happen in real life.

'It's not always about keeping everything hunky-dory, it's about stressing them.'

Although the contract-signing formally took place only this July, Mr Dowdell said BAE had actually been working on the system since the idea was first mooted in 2003, and the basic blueprints for the systems had been drawn up by June 2005.

As well as making sure the dozens of pieces of software, control stations, and other equipment can 'talk' to each other, the trials have been testing the human response to the software in combat situations.

The 23 military operators, largely drawn from HMS Illustrious, were required to respond to a set of lights flashing up on the screen – which was an easy task in peacetime scenarios.

When stressed, they may respond more slowly or not at all, giving analysts an insight into how many people are needed at each terminal – a decision which will be made in the next few weeks.

The new supercarriers will also be the first British ships to have dedicated air traffic controllers, which will control several hundred miles of airspace.

They will also carry flight rehearsal simulators, allowing pilots to fly real-time bomb missions over models of the target.

The combat scenarios used to test the systems revolve around an imaginary territorial conflict between Caledonia and Dragonia – pseudonyms for Scotland and Wales – in which the Royal Navy must enforce UN resolutions.

It is unusual for the end-user to collaborate with the company in the testing of the products, but BAE hopes this will allow it to dispel any misgivings about the system well in advance of delivery.