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The Government Gateway, a site where people register to use more than 100 public services including tax and benefit claims, was temporarily closed after the loss was discovered.
A Department for Work and Pensions spokeswoman said it had ordered an investigation into how it happened.
The stick contained the usernames and passwords of a "handful" of members of the public, although their details were encrypted, she said."Having looked in detail at the stick we are satisfied neither the Gateway nor members of the public have seen their security compromised and the Gateway is online again," the department said in a statement.
The government has suffered a string of data breaches in recent months. They include the loss of secret intelligence files, the details of every prisoner in England and Wales, and information about thousands of potential army recruits.Last year, Prime Minister Gordon Brown ordered a review after HM Revenue and Customs lost data on 25 million people, exposing them to the risk of identity theft and fraud.
Opposition parties and privacy campaigners say the government cannot be trusted with personal information.In the latest incident, the stick was lost by an employee of the IT services firm Atos Origin, which runs the Gateway site for the government.
As well as the log-on details of members of the public, the stick contained information about how an old version of the site was set up.The company said it had disciplined the employee and would work closely with the government and the police in the inquiry.
"It is clear that the employee removed the device from company premises in direct breach of our own operating procedure," Atos said in a statement."The company takes the loss of this device very seriously and we are currently carrying out a full investigation of both the circumstances surrounding its loss and the data content of the stick."