Britain faces fresh accusations that it colluded in the rendering and alleged torture of a second UK resident now being held at Guantanamo Bay. The new claims bring further pressure on ministers to come clean about the scale of the Government's complicity in the rendition and torture of dozens of terror suspects captured by the Americans after 9/11.

His case comes after that of Binyam Mohamed, 30, released from the US naval base in Cuba last week, and whose claims of UK involvement in his torture are being investigated by the Attorney General. Now allegations made by Shaker Aamer, the final British resident held at Guantanamo Bay, raise concerns that both MI5 and MI6 were widely involved in the US rendition and torture programme operated in Afghanistan and Pakistan after 9/11.

Mr Aamer, 42, says he was rendered from the Pakistan border to Afghanistan where he claims he was tortured. He was passed by Pakistani groups to the Northern Alliance who sold him to the Americans. The CIA arranged for his detention in Afghanistan and final transfer to Guantanamo Bay.

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He adds that two MI6 or MI5 officers, a man and a woman, interrogated him after he had been subjected to beatings and sleep deprivation by the Americans while being held at a prison in Kandahar in January 2002. He has told his UK lawyers that the British woman officer called herself "Sally".

A few weeks later he says an MI5 officer was present while he was being tortured by CIA agents in an interrogation cell at Bagram air base in Afghanistan in January or February 2002. This time he claims a man called "John", who introduced himself as being from British intelligence, was in the room when his head was repeatedly "bounced" against a wall and he was told that he was going to die.

Mr Aamer's statement will be used in a High Court challenge against the British government to force ministers to release information about his detention and interrogation in 2002.

The new charges of British complicity in rendition and torture are the latest to be made against the British government which has always denied using torture or helping others use it. But a series of embarrassing revelations has shown the public may not have been told the whole truth. After blanket denials that the British overseas territory of Diego Garcia was used by the Americans for "torture flights", the Foreign Secretary, David Miliband, was forced to admit last year that the UK Government had been misled by the US administration. Mr Miliband said the British outpost on the Indian Ocean island had twice been used by the US as a refuelling stop for the secret transfer of two terrorism suspects in 2002 to Morocco and Guantanamo Bay.

Then, on Thursday, it was the turn of the Defence Secretary, John Hutton, to make an embarrassing admission to Parliament. He told MPs that Britain had helped in the rendition of two Iraqis captured by British forces and sent to Afghanistan for interrogation by US agents as recently as 2004.

Pressure is now growing on the Lord Chancellor and Justice Secretary, Jack Straw, to say what he was told about the US rendition programme when he was Foreign Secretary between 2001 and 2006.

Zachary Katznelson of the human rights charity Reprieve, representing Mr Aamer, said: "We must know whether MI5 or MI6 has information about Mr Aamer's detention and torture so that we can show that any evidence against him obtained under such conditions cannot be relied on by the US in any prosecution."

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Mr Katznelson alleges Mr Aamer had been tortured by American agents for several days before he was interrogated by British intelligence officers. He said: "Mr Aamer has told us that on one occasion he was beaten and his head was bounced against the wall. They were screaming at him 'you are going to die'. He says that during this abuse a member of the British security services was present in the room who witnessed what was happening."

From Bagram, Mr Aamer was flown to Guantanamo Bay, where he is on hunger strike in protest at his alleged mistreatment and continued separation from his family. He also claims to have been beaten and tortured during his detention in Cuba.

Reprieve said the full story of Britain's involvement in US rendition and torture had not been told and that ministers' recent admissions were only the tip of the iceberg.

"This Government has misled us again and again," said Reprieve executive director Clare Algar. "Surely we must immediately have the public inquiry into the Government's conduct of the 'War on Terror' demanded by so many," she said.

Andrew Tyrie MP, the chairman of the All Party Parliamentary Group on Extraordinary Rendition, says the latest revelations require a full inquiry into Britain's role.

Mr Katznelson said Mr Aamer's evidence showed British collusion in rendition and torture was "systemic".

Binyam Mohamed also claims that British agents questioned him before he was sent to Morocco where he says he was brutally tortured before being taken to Cuba. He also said one of the British officers who interrogated him introduced himself as "John".

Mr Mohamed was arrested by Pakistani immigration officials at Karachi airport in April 2002 when intending to return to the UK. He alleges that he was tortured in Pakistan, Morocco and Afghanistan between 2002 and 2004, including being beaten, scalded and having his penis slashed with a scalpel.

The MI5 agent who interviewed Mr Mohamed in Pakistan in early 2002 told the High Court last year that the US and UK both wanted information from him because they regarded him as a terror threat. The question was how it should best be obtained.

A telegram sent by MI5 requesting US permission to see Mr Mohamed made the case that the security service's "knowledge of the UK scene may provide contextual background useful during any continuing interview process ... This will place the detainee under more direct pressure."

In his note of the meeting with the British resident, the MI5 officer recalled: "I told Mohamed he had an opportunity to help us and help himself. The US authorities will be deciding what to do with him and this will depend to a very large degree on his degree of co-operation." Could witness B be the same MI5 agent who Shaker Aamer said had called himself "John"? Or was it coincidence that both British residents came up with same name for their interrogator?

The truth may not be known until Britain releases secret evidence about the Mohamed case. In a ruling last month, the High Court recommended that these documents be made public, but the judges stopped short of making it an order. Lawyers for Mr Miliband had warned that intelligence relations with the US would be seriously harmed were the documents to see the light of day. Lawyers believe these documents may also help to show whether "John", or someone else from MI5 or MI6, also interviewed Mr Aamer.

Mr Aamer, his wife and their three children left London in 2001 to go to Afghanistan to work with a children's charity. But Mr Aamer, a Saudi Arabian national who came to the UK in 1996, was captured on the Pakistan border in December 2001. Mr Aamer was transferred to Kandahar and Bagram air base and then flown on to Guantanamo Bay. For four years he has been held in solitary confinement because the Guantanamo camp guards believe he wields too much influence over other detainees. He has never seen his youngest son, who was born after his capture.

Mr Aamer's lawyers have filed a 16-page claim arguing for his removal from isolation in Guantanamo Bay prison. The British government has recently begun pressing the US administration for Mr Aamer's release.

It is understood that a party of Foreign and Commonwealth Office officials who visited Mr Mohamed in Cuba shortly before he was cleared for release, also had limited contact with Mr Aamer, who has lost half his body weight after a series of hunger strikes. An FCO spokesman said the Americans had told the British Government that they still had security concerns about Mr Aamer and would not release him.

A spokesman for the Foreign and Commonwealth Office said that they took Mr Aamer's allegations very seriously and had launched an "urgent review" of the case. He said that Britain did not carry out or collude in torture.

How the Government changed its story from denial to regret

No one told us

20 November, 2005

"These are privately chartered aircraft and they don't need to tell us who is on board."

Department of Transport

We don't keep track of such things

22 November, 2005

"Where passengers do not leave the airfield, the MoD ... does not record details of passengers."

Adam Ingram, then Defence minister

No one asked us

30 November, 2005

The Government is "not aware of the use of their territory or airspace for the purposes of extraordinary rendition, nor have we received any requests, [or] granted any permission for the use of UK territory or airspace for such purposes".

Foreign Office

It never happened

5 December, 2005

"We have no evidence to corroborate media allegations about use of UK territory in rendition operations."

Foreign Office

We have no record

13 December, 2005

"Careful research has been unable to identify any occasion ... when we have received a request for permission by the United States for a rendition through the United Kingdom territory or airspace .... Unless we all start to believe in conspiracy theories ... there is simply no truth in claims that the UK has been involved in rendition."

Jack Straw, then Foreign Secretary

There's no evidence

22 December, 2005

"I have absolutely no evidence to suggest that anything illegal has been happening here at all.

"I am not going to start ordering inquiries into this, that or the next thing when I have got no evidence to show whether this is right or not."

Tony Blair, then Prime Minister

We've done nothing illegal

20 January, 2006

"Anything we do in relation to rendition is in compliance with our international obligations. We fulfil our legal obligations."

Tony Blair's spokesman

They'd have to ask us first

16 February, 2006

"We have made clear to [the US] we expect them to seek permission to render detainees via British airspace."

Ian Pearson, then Foreign Office minister

We've never given permission

7 October, 2006

"Mr Hoon ... made clear that the British Government has not approved and will not approve a policy of supporting the transfer of individuals through the UK to places where there are substantial grounds to suspect that they face the risk of torture."

Foreign Office

OK, they did it twice. But that's all

25 February, 2008

"The two flights from the US already identified are the only ones we are aware of."

Foreign Office

Yes, we were involved. And we shouldn't have been

27 February, 2009

"In retrospect, it is clear to me that the transfer to Afghanistan of these two individuals should have been questioned at the time."

John Hutton, Defence Secretary