The Department of Health is seeking an explanation from CSC over allegations the supplier was involved in the illegal rendition of European citizens in the US "war on terror".
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CSC has been accused of organising the flights of people between secret prisons where they were alleged in some cases to have been tortured.
"We are concerned by these allegations and plan to seek clarification from CSC," said the Department for Health in a statement to Computer Weekly.
The department and the UK Cabinet Office are in the middle of protracted negotiations with CSC over its failure to deliver IT systems to the NHS National Programme for IT. The coalition government had been trying to scrap the NHS programme but has been unable to renegotiate the contract with CSC. A resolution is expected in August – although previous deadlines for an agreement have been missed.
Human rights charity Reprieve is writing to CSC customers after it unearthed documents it claims prove the IT supplier managed rendition flights for the US Central Intelligence Agency (CIA). Invoices allegedly show CSC was contracted to charter flights in one case, where the CIA transported German citizen Khaled El-Masri after his abduction from Europe and secret imprisonment in Afghanistan.
But other CSC customers are choosing to disregard the allegations.
"It's not our policy to comment on things like that," said a spokesman for ArcelorMittal, the world's largest steel producer, which outsourced its IT to CSC in July 2011.
Transport for London (TfL), which in January renewed a CSC contract on which it has spent £100m since 2006, said: "TfL was not aware of the allegations made against CSC.”
Reprieve has written to TfL and its chairman, London mayor Boris Johnson. TfL has so far declined the opportunity to respond to further questions from Computer Weekly.
A spokesman for Royal Mail, which has outsourced its IT to CSC since 2003, said: "We do not comment on our commercial relationships with our customers and suppliers."
The Ministry of Defence (MoD) said it had sought an explanation from CSC after giving it a seven-year, £400m contract in April to run the British Service Personnel and Veterans Agency system, which handles approximately £14bn in pay and pensions every year.
The procurement process included a "good standing" assessment, to tell if bidders had committed criminal offences or acts of grave professional misconduct that might bar them from working with UK armed forces.
An MoD spokesman said: "We looked for assurances from CSC following these allegations from Reprieve.
"They provided an assurance that CSC has a robust corporate responsibility programme that includes an affirmative human rights statement."
The MoD was led to believe the allegations centred on DynCorp, a company CSC acquired in 2003 and sold in 2005.
Dr Crofton Black, a researcher for Reprieve, said the charity had discovered invoices connecting CSC with likely rendition flights up to mid-2006, after it sold DynCorp.
CSC acquired DynCorp along with 40 subsidiaries and 26,000 staff for $950m in 2003. CSC subsequently won a contract to supply DynCorp security personnel to support the US invasion of Iraq and became the fourth largest contractor to occupying US forces. But CSC sold part of DynCorp subsidiary DynPort for $850m after it was rebuked by the US State Department for the aggressive behaviour of its guards protecting Afghan leader Hamid Karzai.
CSC remained the 92nd largest contractor in Iraq after the sale and retained parts of DynCorp including DynPort, which produces biological warfare vaccines under contract to the Ministry of Defence and US Department of Defense.
Reprieve claims CSC also retained its rendition contracts.
CSC said in a statement that it retained the name DynCorp but subsumed its retained divisions, particularly DynCorp Technical Services, which became CSC Applied Technologies, and provides security and operates test ranges for US military bases. Other DynCorp subsidiaries were sold or discontinued.