The Ministry of Defence has expressed concerns that some wind farms interfere with military radar, making aircraft flying over the turbines "invisible".
A radar's line-of-sight can be impaired by wind turbines
But it denies opposing every planning application for new wind farm sites, saying there are many factors involved.
Government energy officials say they are working with the MoD to resolve problems over the issue.
It follows the government's announcement of plans to increase the number of homes powered by wind farms.
Tests in 2004 and 2005 showed that wind turbines create a "hole" in radar coverage.
The shadow of the blades is magnified considerably, and the movement of the propellers is visible on radar screens.
The Royal Air Force says it has to be able to detect all aircraft flying into areas covered by its radar for safety and security reasons.
Air Chief Marshal Sir Jock Stirrup, the Chief of the Defence Staff, has insisted that radar capability must not be impaired.
But a spokesman for the MoD denied that every planning application for a new wind farm was opposed - saying that there are many factors that have to be borne in mind when a site is suggested.
The MoD also confirmed it is working with wind farm developers to find a "mutually acceptable solution" including providing input on turbine design and materials to reduce the problem in its new T102 radar system.
The Department for Business, Enterprise and Regulatory Reform (BERR) is responsible for energy policy in the UK. It says it recognises that issues concerning military radar can arise in planning applications for wind farms.
"We are working with the MoD to explore technical and other potential solutions to try and resolve radar issues where these arise," said a spokesman.
The department adds that it is working with the MoD, civil airport operators and National Air Traffic Control "to identify... solutions to mitigate the interference of wind turbines on their radar installations".
In December the Business Secretary, John Hutton, announced plans which could lead to every household in Britain being powered by a wind farm.
Under the proposals, up to 7,000 turbines could be installed to boost wind produced energy 60-fold by 2020.
At present, wind farms only produce enough power for about 375,000 homes.