Archie Graham, the deputy leader of Glasgow City Council and its spokesman on the Games, defended the French IT giant at the Scottish Labour conference in Inverness.
The company will supply the software to accredit up to 70,000 athletes, volunteers and officials, and run the Glasgow 2014 website.
Disability rights campaigners want Atos dropped as sponsor because of the key role played by its offshoot, Atos Healthcare, in the Coalition's welfare reforms.
Atos Healthcare has a £110 million annual contract with the Department of Work and Pensions to run work capability assessments of the sick and disabled, and a £400m deal to assess mobility benefits.
Critics say the tests are flawed, degrading and inefficient, with one in six passed as fit to work winning an appeal against the decision.
Graham said: "They are particularly good at organising IT infrastructure. You can be absolutely assured we'll be working very hard to ensure that Atos won't use the fact they have a connection with the Games in any inappropriate way whatsoever."
But Marie Garrity, of Unison, told delegates: "Atos are a pernicious organisation who profit from inflicting suffering on the poor. Let's not give them the opportunity to use our Games as a chance to try to pass themselves off as decent corporate citizens. Let's keep the pressure on the Scottish Government and the Games organisers to bin Atos as sponsors. That way we can have a Commonwealth Games that we can all be proud of."
The SNP have also been criticised in the past over the Atos sponsorship of the Games. Deputy First Minister Nicola Sturgeon last year hailed the deal as "a significant step forward for the Games".
Another delegate said that as a disabled person she was "really upset about Atos's involvement," and asked for an assurance that their role will be treated cautiously by organisers.