The Ministry of Defence awarded CSC a £303m contract after learning of allegations the supplier was involved in the illegal rendition and torture of German citizen Khaled El-Masri.
The department dismissed the allegations as irrelevant, saying procurement rules prevented it from allowing them to affect its decision on whether to award CSC the contract, a seven-year deal to administer pay and pensions for 1.25 million armed forces personnel.
Human rights charity Reprieve told defence personnel minister Andrew Robathan about the allegations on 25 April 2012, within two weeks of news emerging that the Ministry of Defence (MoD) had picked CSC as preferred bidder among shortlisted suppliers that had tendered for the £303m contract.
Reprieve told Robathan it had documentation "linking [CSC] to torture, secret detention and extraordinary rendition".
Cori Crider, legal director of Reprieve, said in the letter that CSC had refused to renounce torture, and asked "whether the MoD believes it is appropriate to do business with a company that refuses to make a simple pledge that it will not be complicit in the crime of torture."
In a letter that she also sent to Air Vice-Marshal Ross Paterson, chief executive of the Service Personnel and Veterans Agency (SPVA), the MoD body handling the contract, Crider asked: "[Was] CSC’s involvement in torture and secret detention taken into account during the bidding process."
The minister replied a month later, through the SPVA, that procurement rules forbade the MoD from allowing the allegations to influence its decision to award the contract. It awarded the deal on 8 June, six weeks after it was asked to take the allegations into account.
"The allegations made would not fall into the category of conduct which would be capable of consideration in this particular context and the MoD is unable to take them into account," said Brigadier Geoff Nield, SPVA head of strategy and programmes, in a letter on behalf of the minister and Paterson on 24 May.
Nield said the MoD was not allowed to ask suppliers about their policies "on general issues not related to the subject matter of the contract", nor could it take unrelated matters into account when awarding a contract.
The SPVA did, however conduct a "good-standing" assessment of CSC before appointing it as preferred bidder in April. This process checked whether the supplier had committed criminal offences or acts of "grave professional misconduct" that would exclude it from bidding.
The MoD did not know about the allegations when it conducted the good-standing assessment, said an MoD spokeswoman. The department asked CSC for an explanation after Reprieve raised the allegations on 25 April. CSC told the MoD it had a corporate social responsibility programme that included a statement about human rights.
The spokeswoman declined to say whether MoD was satisfied with CSC's response. She said MoD had not conducted another good-standing assessment of CSC after the "torture flight" allegations had emerged.
Nield told Reprieve that CSC had been given a gold ranking in a corporate responsibility index by Business in the Community, a UK charity. The charity said the award had been given in respect of a self-assessment questionnaire, and that CSC's answers were confidential.
Reprieve is writing to other CSC customers, urging them to boycott the supplier over its alleged involvement in CIA rendition flights. The NHS, which has a controversial deal with CSC as part of the now-defunct National Programme for IT, told Computer Weekly it is "seeking clarification" from the supplier about the allegations.