The incident is the latest in a series of embarrassing revelations concerning police and customs officers which are underminding the war on organised drugs smuggling.
Each of the stolen files would have contained intelligence reports on major drug traffickers, with names of informants and police and customs officers working on the operation.
A Customs spokesman said: "We have taken what steps we can to minimise the damage caused to any operations in which the officer was involved."
A report will be sent to the Crown Prosecution Service next week on one of Britain's most disastrous drugs investigations.
Detectives from Thames Valley police have spent two years and eight months on the relationship between one of the country's biggest drugs barons, a Tory MP and police officers.
The investigation, codenamed Operation Mantis, was ordered by the Police Complaints Authority after the collapsed prosecution of Brian Charrington, the mastermind of the import of 1.5 tonnes of cocaine into Teesside in 1992. The report will also refer to Tim Devlin, MP for Stockton South.