The UK government approved the 2004 rendition of a terror suspect to the Gaddafi regime, the BBC can reveal.
A letter from an MI6 officer refers to Abdel Hakim Belhaj's rendition to Libya. It congratulates the Libyans on the "safe arrival" of the "air cargo".
Mr Belhaj says he was tortured in jail. Successive UK governments have denied complicity in rendition or torture.
But BBC correspondent Peter Taylor says he understands Mr Belhaj's rendition was given ministerial approval.
However it is not clear at what level of government the decision was authorised.
The letter from the senior MI6 officer, Sir Mark Allen, to Col Gaddafi's intelligence chief, Musa Kusa, was found last year in the rubble of Musa Kusa's headquarters, which were bombed by Nato.
As well as congratulating the Libyans on the arrival of the "cargo", it points out that "the intelligence was British".
The letter was sent in 2004 when Mr Belhaj was the leader of the Libyan Islamic Fighting Group.
MI5 believed the group was close to al-Qaeda and involved in recruiting young Muslims in Britain to fight in Iraq.
Our correspondent says it appears MI6 had discovered that Mr Belhaj was in Malaysia and about to head for London in the hope of obtaining political asylum.
MI6 informed its foreign intelligence partners, and as a result Mr Belhaj was intercepted in Bangkok, presumably by the CIA, and rendered to Libya.
Our correspondent says the letter suggests MI6 was complicit in Mr Belhaj's illegal rendition and alleged torture in Libya - but that MI6 was not acting unilaterally.
He says his understanding is that MI6 obtained authorisation from the Labour government of the time for its action.
Jack Straw was the Labour Foreign Secretary in 2004 when the rendition took place. In an interview on BBC Radio 4 last year he said: "We were opposed to unlawful rendition. We were opposed to any use of torture or similar methods. Not only did we not agree with it, we were not complicit in it and nor did we turn a blind eye to it."
He added: "No foreign secretary can know all the details of what its intelligence agencies are doing at any one time."
His office told the BBC Mr Straw had nothing further to add in the light of the current allegations.
Mr Belhaj - now a senior military commander in the new Libya that Britain helped create - is suing MI6 and the British government, accusing them of complicity in his illegal rendition and alleged torture.
He says he believes he was rendered from Bangkok to Libya by the CIA.
The Metropolitan Police is also investigating his allegations.
Mr Belhaj worked with Nato as one of the leaders of the forces that helped overthrow Col Muammar Gaddafi.
But he claims that during his more than four years in prison he was interrogated by agents from countries including the UK and US.
He had been living in exile in Beijing after leading opposition to Col Gaddafi.
Former foreign secretary Sir Malcolm Rifkind, who now chairs the Intelligence and Security Committee, said the report is a cause for great concern.
He said: "It's very worrying indeed because if he was rendered to Libya and if the United Kingdom intelligence agencies and the United Kingdom government were involved, that is not only contrary to the policy that the British government has pursued for a long number of years, but also to assurances that were given to the intelligence and security committee as well as to Parliament as a whole."
In 2010, Prime Minister David Cameron established a detainee inquiry into "whether Britain was implicated in the improper treatment of detainees, held by other countries, that may have occurred in the aftermath of 9/11".
However, the inquiry was mothballed in January 2012 after the Metropolitan Police announced it was investigating Mr Belhaj's claims.
Justice Secretary Ken Clarke said the government was committed to holding a judge-led inquiry once these were investigated.
Watch Modern Spies on BBC 2 at 21:00 BST on Monday 9 April for more on this story.