The Foreign Office said it was only recently discovered that records of flights passing through an overseas territory used by the US for extraordinary rendition had been lost to "water damage".
A spokeswoman said:
The British Indian Ocean Territory administration is responsible for records of flights on Diego Garcia and they are investigating the full extent of the damage, how many records and what information is affected.
The damage was only recently discovered so it is unknown how exactly or when it occurred.
More top news
Oxfam have released a 10-year review accessing the impact of their work after the Tsunami.
British pubs are still considered cornerstones of the community, but with an estimated 30 closures a week, is this tradition under threat?
The remarkable rescue of baby elephant Roi, who faced starvation after poachers killed its mother, was captured on film.