The move will bring the two plants in Berkshire - the scene of 1960s peace demonstrations - under the same inspection rules as Britain's civil nuclear plants, such as Dungeness and Sellafield.
John Spellar, the defence minister said: "This will provide independent assurance that nuclear related activities at the Atomic Weapons Establishment are carried out safely and pose no threat to the workforce, the public or the environment."
Anti-nuclear campaigners believe the inspectorate is likely to fail the sites, because of the growing stockpiles of nuclear waste, which are increasing after the Nirex application for a deep depository at Sellafield, Cumbria, was turned down.
"There are increasing amounts of nuclear waste on the sites. They also have at Aldermaston buildings which are entirely contaminated and closed. We believe they have 3,000 tons of intermediate nuclear waste stored on site," said a spokesman for the Campaign for Nuclear Disarmament.
The Health and Safety Executive investigated the plant at Aldermaston in 1994 and expressed some concern about waste management problems.