The disks stored data from the Service Personnel and Veterans Agency
The government has kept secret the loss of highly sensitive RAF vetting records, which one wing commander says leaves individuals open to blackmail.
Last September the Ministry of Defence (MoD) said data on tens of thousands of personnel was lost from RAF Innsworth in Gloucestershire.
Some 500 files with details of affairs, debt and drug use were also lost, BBC Two's Who's Watching You? will say.
The MoD said there was no evidence that criminals had targeted the data.
It was said the discs the MoD admitted to losing were taken from a secure area, and included names, addresses and some bank account details.
Vetting is the process of assessing an individual for higher security clearance.
They'd ask you questions such as: is there anything unusual about your sex life? Have you had affairs? Used prostitutes? That sort of thing
Former RAF officer
An internal MoD memo - obtained by a former officer and passed to BBC Two's Who's Watching You? programme - shows the lost files contained "details of criminal convictions, investigations, precise details of debt, medical conditions, drug abuse, use of prostitutes, extra-marital affairs including the names of third parties".
The e-mail - from an unnamed wing commander - says the data "provides excellent material for Foreign Intelligence Services and blackmailers".
In the memo, written three weeks after the disks were stolen, he added: "By not declaring that highly sensitive vetting information has been lost, I am concerned that we, the RAF, will be accused of attempting a cover up."
The man who obtained the memo is a former serving RAF officer. He regularly worked with top secret and highly sensitive information.
Former RAF officer: staff 'could be open to blackmail'
He has been through the vetting procedure and told the BBC it was a gruelling process.
"They'd ask you questions such as: is there anything unusual about your sex life? Have you had affairs? Used prostitutes? That sort of thing. If the information got into the wrong hands then it could leave people wide open."
The MoD did admit the data loss incident but failed to announce the vetting details were lost.
The Information Commissioner's Office says it was not informed of the loss of such sensitive data. Parliament was not told about its loss either.
In a statement, the MoD said it treated all personal data seriously, and had spoken to those potentially affected.
"All individuals identified as being at risk received personal one-on-one interviews to alert them to the loss of the data, to discuss potential threats and to provide them with advice on mitigating action," the statement says.
"There is no evidence to suggest that the information held on the hard drive... has been targeted by criminal or hostile elements."
Who's Watching You? starts on 25 May at 9pm on BBC Two and will also be available on BBC iPlayer.
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