The payments were made as Sir Peter Ricketts, the National Security Adviser, warned that spending cuts could damage morale in the intelligence services and threaten security.
Details of the payments are contained in the accounts for the security and intelligence agencies, which were published this week.
They show that the agencies spent £13.7 million on “losses and special payments” in the 12 months to the end of March this year.
A note to the accounts says the sum was swelled by “an SIA [Security and Intelligence Agencies] contribution to a payment in respect of legal claims in excess of £250k”.
The actual figure paid to the Britons is not given, because of a confidentiality agreement with the lawyers of the former terrorist suspects.
It is thought that around £12million is likely to have been paid to the Guantánamo Bay suspects.
This is because the agencies have on average spent £1.5 million a year on losses and special payments over the past five years. The total compensation figure paid to 16 Britons who were suing the Government is likely to be around £14 million, and will have been swelled by payments from other government departments.
The former detainees have denied wrongdoing. In April, The Daily Telegraph disclosed for the first time details of the US accusations against the men, which were contained in files compiled about them in Guantánamo Bay.
In the accounts report, Sir Peter warned that spending cuts posed “risks to staff morale and security”. He wrote: “Like other Government departments, the agencies have or are currently undertaking workforce rationalisation strategies which could result in associated risks to staff morale and security.’’
He added: “The Agencies also face a challenge in that they must ensure their internal control systems are able to manage the significant increase in activity associated with the London 2012 Olympics. Preparations for this are in the advanced stages.”
Last night Patrick Mercer, a senior Tory MP, said: “I hope that this was the right decision to pay suspects at the same time as not rewarding our own agents in the way that they should be. Quite rightly their work is not obvious, but our intelligence agencies are stunningly successful and anything that hits their morale and efficiency has got to be very seriously questioned.’’
A Cabinet Office spokesman said: “For legal reasons we cannot comment on the details of any settlement the Government came to with former Guantánamo detainees.’’
The legal settlement was first announced by Kenneth Clarke, the Justice Secretary, to the House of Commons last November.
The sums were paid not just to the detainees who brought legal action against the government but to an additional four who were not involved in the court cases but could have sued.
The men had claimed that the Government had allowed them to be sent to be mistreated at the US detention centre in Guantánamo Bay.