In one of the worst episodes, live and potentially lethal mustard gas bombs were found next to a working factory years after the site was supposed to have been cleaned up. Yet a confidential Ministry of Defence memorandum shows that this was hushed up to avoid "local public reaction" to what it describes as "an extremely sensitive issue".
Pollution of defence land - which, in total, covers an area the size of the Lake District - is still kept secret. Ministers refuse to list the sites which store toxic and radioactive wastes, to give details of dangerous pollutants discharged, or even to describe the extent and cost of clean-up measures.
But Michael Meacher, the shadow environment secretary, has been collecting evidence that he says "suggests that for many decades there has been a significant problem of contamination associated with military bases in the UK".
The official check-up, the first ever systematic survey of the problem, aims to "establish the condition of the individual sites on the defence estate and, where appropriate, make recommendations for, and implementation of remediation". As there are 800 such sites in England and Wales alone, those thought to be most dangerous are being investigated first.
One of these is RAF Barnham, near Thetford in Norfolk, where last year a ministry Estates Office (EOD) team found 17 live mustard gas bombs in an area supposedly "cleared" by the official Property Services Agency many years ago.
An extraordinarily frank internal memorandum, reporting the discovery, signed by Squadron Leader C J Oxland, continues: "As far as we are concerned this is largely a matter of 'wait and see'.
"The most significant problem that we may encounter is local public reaction ... The site is next door to a factory, one of the managers of which is an ex-RAF armourer who the EOD team regard as their biggest threat ... he has just enough knowledge to be dangerous in PR terms."
Chemical warfare experts said last week that the gas would have been extremely dangerous if it had leaked out. The ministry said that the site had now been cleared and was up for sale.
Other incidents collected by Mr Meacher include:
n Pollution by mustard gas and other contaminants at a former Second World War chemicals factory at Mold, Clwyd, now used as a storage depot by the Ministry of Agriculture.
n The closure of 94 acres of woodland at Risley, Berkshire, last year after mustard gas was found to have been dumped there. Contamination by the gas, at 130,000 times above tolerable levels, was found - even though the site had been declared safe by the ministry in 1988.
Other evidence suggests that more than 60 sites across the country are contaminated by the poison gas, which remains active for decades.
Military bases have long enjoyed "Crown immunity", freeing them from possible prosecution by pollution inspectorates or from civil actions for damages. This, critics say, encouraged lax practice.
But pressure on the ministry to come clean is now mounting because military land is increasingly being sold off and privatised.
Mr Meacher says: "The Government is notably reluctant to publicise any information about contamination on military bases. Much relevant information is either secret or inaccessible. It is complacent about problems it has inherited from the past, secretive about current activities, and unsystematic about the collection of vital evidence. National security has been used as a convenient cover for bad practice."