In April 1957, five unmarked lorries left the British High Commission in Kuala Lumpur and drove to a Royal Navy base in Singapore with their cargo of files detailing the secrets of Britain’s rule in Malaya. Their destination was, in the words of one official, a “splendid incinerator”.

This “discreet” mission in the closing days of British rule over what became Malaysia was one of hundreds of similar operations. As the sun finally set on the Empire, diplomats scurried to repatriate or destroy hundreds of thousands “dirty” documents containing evidence that London had decided should never see the light of day. Some 50 years later, the sheer scale of the operation to hide the secrets of British rule overseas – including details of atrocities committed during the Mau Mau rebellion in Kenya – is revealed in documents released today by the National Archives in Kew, west London.

The so-called “migrated archive” details the extraordinary lengths to which the Colonial Office went to withhold information from its former subjects in at least 23 countries and territories in the 1950s and 1960s.

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Among the documents is a memo from London that required all secret documents held abroad to be vetted by a Special Branch or MI5 liaison officer to ensure that any papers which might “embarrass” Britain or show “racial prejudice or religious bias” were destroyed or sent home.

The ramifications of the operation to conceal the resulting archive of 8,800 files – a closely guarded Whitehall secret until the Government recently lost high-profile court cases – are still being felt in compensation claims for victims of atrocities committed under British rule from Kenya to Malaya.

Relatives of 24 Malayan rubber plantation workers allegedly murdered by British soldiers in the Malayan village of Batang Kali in 1948 returned to the Court of Appeal this week to try to overturn a ruling that the British government cannot be held responsible for the massacre.

Most of the records of the original investigation into the killings were destroyed, most likely during the eight-month period that included the sending of the lorries to Singapore.

A memo recording the destruction operation in 1957 notes that the MI5 liaison officer overseeing the operation believed that as a result “the risk of compromise and embarrassment [to Britain] is slight”.

John Halford, of the law firm Bindmans, which is representing the Batang Kali relatives and victims, told The Independent:

“British officials through the years have been desperate to consign the Batang Kali atrocity to history, despite those who were there as children still being very much alive and driven to seek justice.”

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Known in several former colonies as “Operation Legacy”, Whitehall set out a list of the types of material it wanted removed, including anything which “might embarrass members of the police, military forces, public servants (such as police agents or informers)”. Once “dirty” documents had been removed the remaining “clean” material was passed to a new strata of administrators overseeing independence processes who were deliberately not told about the sifting process.

It also ordered the destruction or removal of “all papers which are likely to be interpreted, either reasonably or by malice, as indicating racial prejudice or bias”.

Under the rules, all material marked “Top Secret” or “Secret” was either sent back to Britain via the RAF or the navy, or destroyed either by burning or “placed in well-weighted crates and sunk in deep and current free water at the maximum practicable distance from shore”.

Among the documents is a note that officials should carefully control any bonfires of secrets and avoid a situation similar to Indian in 1947 when the local press was filled with reports about the “pall of smoke” which fell over Delhi at the end of the Raj as British officials burnt their papers.

The files show that in the months before Kenya gained independence in December 1963, some 307 boxes of material were sent back to Britain.

The evidence remained hidden for five decades until court cases brought on behalf of victims of brutality forced its disclosure last year and a subsequent £20m pay out and apology from the Foreign Secretary, William Hague, this summer.