To the team from the Air Warfare Centre, a jaunt to rural Wales to monitor the effect of wind farms on radar should have been a routine and pleasant mission.

Two elderly RAF planes were spared for the experiment and their pilots ordered to do figures-of-eight around some windmills to see if they were visible as dots on screens.

The defence experts discovered an alarming threat to national security from wind farms which now seriously jeopardises the expansion of this mode of green energy. Experts knew that there was a tiny area around wind farms where low lying planes are difficult to see by radar and this exercise was designed to measure the extent of the problem.

One of the team noticed an aeroplane, not part of the experiment, which was flying over the turbines but failed to be picked up on the screens.

The pilots of the Chinook HC Mk 2 and Tucano T Mk 1 were given new orders to fly directly over the Llandinam wind farm in South Wales at various altitudes. The planes became quite invisible. A follow-up experiment confirmed that there is a blind spot over wind farms which makes aircraft undetectable by radar.

The discovery has left ministers with a dreadful dilemma. Britain is relying on a huge increase in wind power to help to reduce carbon emissions and so meet targets to prevent catastrophic climate change. But the defence of the skies has become all the more urgent since 9/11 when terrorists shocked America by commandeering four commercial flights.

President Bush has claimed that the CIA foiled a massacre plot to crash aircraft into the towers of Canary Wharf in East London. If the RAF has to be scrambled to save Britain from such peril, every second of advance warning will count.

The revolution in the Ministry of Defence’s thinking on radar air defence was disclosed by Squadron Leader Chris Breedon in his evidence opposing a new wind farm in North-umbria. “Traditionally, the primary role of the Air Surveillance and Control System has been to detect aircraft approaching the UK from overseas. However, equal, if not more, importance is now given to monitoring UK airspace to detect, track and respond to any aircraft which is giving concern.

“The significance of the low-level radar cover has risen markedly as a result of the terrorist events of September 11, 2001. The MoD is extremely concerned with any proposed wind turbine development which would have an impact on the . . . system.”

Put simply, the operators are less worried about looking for enemy aircraft approaching from overseas. The real threat is over our heads. The full results of the tests remain classified.

Wind farms confuse radar because the turbines are mistaken for planes. They are high and have rotating blades which can mimic the effect of aircraft when detected by radio waves. The British Wind Energy Association says that the existing 165 farms produce enough energy for 1.3 million homes and save 5 million tonnes of carbon a year. Ministers were faced with a choice of disasters to avert. Mass terrorist attack or calamitous rise in temperatures?

The MoD is raising last-minute objections to wind farms at Hexham and Kirkwhelpington in Northumberland, Berwick-upon-Tweed and the Lammermuir Hills in the Scottish Borders, Routh in the East Riding of Yorkshire, Thorney near Peterbor-ough and Ceres in Fife. Campaigners for wind farms are suspicious that the MoD has adopted a hardline policy some time after the scientific evidence was discovered. Experiments which found that radar has blind spots over wind farms were completed in September 2004 and April 2005. In May 2005 the MoD confirmed it had no objections to a proposal for 62 turbines up to 125m high at Fallago Rig in the Lammermuirs. But in March 2007 it objected to a smaller plan for 48 turbines.

The MoD said in documents for a public inquiry: “The [air surveillance system] has received firm direction from the Chief of the Defence Staff on the minimum acceptable surveillance coverage and this informs the objection to the wind turbine development. That directed surveillance coverage is required to undertake counter-terror-ist operations against airborne threats and allow tactical decisions to be taken as situations develop. A degraded or inaccurate picture could delay, or even negate, appropriate actions.”

The blind spots can arise even at long distances from radar stations and the MoD is studying all proposed wind farms in the “line of sight” of their monitors. The ministry declined to say how far the line of sight can be.

Security objections threaten to scupper the new age of wind power. Yet in December the Energy Secretary, John Hutton, announced that Britain wants a 60-fold increase in wind energy by 2020. A new radar system called T102 is due to be introduced in two of Britain’s six monitoring stations – at Trimingham in Norfolk and Brizlee Wood in Northumberland.

The Chief of Defence Staff’s insistence that there must be no degradation of radar cover appears irreconcilable with the country’s energy ambitions. So The Times asked the MoD if it had been given a copy of Mr Hutton’s announcement for advance clearance. A spokesman replied: “We’re in close consultation.”

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