The Ministry of Defence is blocking 13 wind farm developments from the Scottish borders to the Caithness coast because it claims they could create radar "blind spots" which might allow hostile aircraft, cruise missiles or even hijacked passenger jets to creep in under the country's protective screen.

It has also lodged objections to 29 other proposed turbine sites in England, including four backed by the Department for Business, Enterprise and Regulatory Reform, one of the bodies responsible for pushing forward the government's renewable energy strategy.

Included in the list of sites in Scotland is the Eskdalemuir seismological reporting station, used as part of a global chain to monitor the shockwaves from nuclear explosions anywhere on the planet.

The MoD fears the vibration from giant turbine blades on a nearby wind farm could affect the station's delicate sensors.

The radar problem caused by wind farms was discovered by accident in 2004 during UK Air Warfare Centre tests over a Welsh site. The RAF found to its shock that the spinning blades produced "clutter" on radar screens mimicking the signature of propellor-driven aircraft.

More alarmingly, it also turned an area three miles out to sea and 5000ft above the site into what one officer described as "a zone of invisibility" and triggered nightmares of possible vulnerability to 9/11-style airborne terrorist suicide attacks.

Nato and the Pentagon were also unaware of the potential hole in their defences caused by the green revolution and have since taken measures to limit developments throughout Europe and the US.

The MoD has now awarded a contract to BAe Systems, the UK's biggest defence contractor, to develop computer software capable of separating turbine blades from aircraft on a radar screen in much the same way as naval radar can differentiate sea-skimming missiles from flocks of seabirds.

In a statement, the MoD said: "We fully support the government's renewable energy policies and consider each development proposal on a case-by-case basis. We are always ready to consider mitigation measures, such as changing the height or number of turbines, or slightly changing their location where agreeable if that would allow a development to go forward."

The reasons given for the 13 Scottish objections to site development include interference with air-defence or air traffic control radars, unacceptable restriction on low-flying training, and interference to seismological instruments.