The company announced that it was seeking an early withdrawal from the Department for Work and Pensions work capability assessment contract, after a series of protests outside 45 ATOS offices over the way assessments have been conducted. The contract was due to end in August 2015.
Prospect National Secretary Geraldine O'Connell said: "Sadly, it is our members who are delivering this contract and have been caught in the crossfire.
"Already they have felt themselves to be the scapegoats of government policy and borne the brunt of criticisms that should have been addressed to the DWP and the government.
"Now they face even more uncertainty as the contract comes up for review."
There have been persistent personal and online death threats against the ATOS Healthcare staff who conduct assessments on sick and disabled people. Based on their reports, the DWP then decides who is eligible for benefits.
About 163 incidents of the public assaulting or abusing staff were recorded each month last year, Atos told the Financial Times.
The French IT company said it viewed the current contract as 'outdated' and not working for claimants, the DWP or ATOS Healthcare. The political environment had become untenable and it was no longer fair to employees to leave them vulnerable to attack.
Prospect is not yet clear how the DWP will redesign any new contract for 2015 – possibilities include a single contract across the UK or a series of regional arrangements.
"Either way, it is going to be a huge logistical challenge to transfer this work, and all the attendant IT support to a new provider," said O'Connell. "For this reason alone, this is unlikely to be a quick process."
Prospect is providing advice to members about the application of the Transfer of Undertakings (Protection of Employment) Regulations if they are transferred to another company.
TUPE regulations apply to organisations of all sizes and protect employees' rights when the business they work for transfers to a new employer.
O'Connell said Prospect would be party to all consultation arrangements, once a company has been chosen for the new contract.
Atos has been the sole provider of the benefits contract since 1998, when the then Labour government first gave this work to the private sector. The company earns revenues of £110m a year from the current arrangement.