Campaigners plan to turn the Queen's Baton Relay, the equivalent of the Olympic Torch relay, into a public-relations disaster if Atos is involved when the Games start, with pensioners and wheelchair-users potentially being arrested for blocking the route.
It comes as Games organisers are forced to review security costs after the spiralling bill at the London Olympics. Just 5%, or £27 million, of Glasgow 2014's £524m budget is earmarked for security. Policing and security in London exceeded 10% of the budget.
The Scottish Government will warn Holyrood's Audit Committee this week that "a range of budget pressures have been identified" around security.
A report to MSPs also reveals the Commonwealth Games Federation has demanded "clarity on security arrangements and budgets" after a visit to Glasgow by its officials in October.
The Audit Scotland watchdog has already warned the £27m for security in 2014 may be insufficient. Most bills for the Games are split 80-20 between the Government and Glasgow City Council, but extra security costs fall on the Government.
French IT giant Atos became a Games sponsor in March. It will supply software to accredit 70,000 athletes, officials and volunteers, and run the Games website. It also sponsored the London 2012 Olympics.
But the work of an Atos offshoot is highly controversial. Atos Healthcare has a £110m-a-year contract with the Department for Work and Pensions to run Work Capability Assessments to see if sick and disabled people are fit to work.
Critics say the tests are flawed, degrading, and meant to cut benefit spending.Around one in six of those assessed as fit to work by Atos successfully appeals the decision, costing taxpayers extra £50m extra a year.
Around 25 protesters invaded Glasgow 2014's HQ last Tuesday. More protests are planned this week, and the ultimate plan is if necessary to disrupt the Queen's Baton Relay.
The relay has been the curtain-raiser to every Commonwealth Games since 1958. It will visit all 32 Scottish council areas over 40 days and is a potential money-spinner, with TV coverage making it attractive to sponsors. That could be wrecked by protests.
The security bill for the London Olympics rose from £600m to £1 billion, and security costs also went up at the Commonwealth Games in Manchester in 2002 and in Melbourne in 2006.
Sean Clerkin of Citizens United, the group behind last week's occupation, said: "We support the Games and we want them to be a success, but if Atos are still a sponsor in 2014 we will disrupt the relay in no uncertain terms. We will disrupt it with people who are pensioners, who are disabled, who are vulnerable.
"It doesn't matter how they crank up the security, we will disrupt it – are they going to arrest elderly people, people in wheelchairs?
"Now is the time for the Games to take a step back and look at the criticism of Atos and withdraw them – they are not a fit and proper company to be a sponsor in a civilised country like Scotland, because of what they are doing to poor, disabled and vulnerable people."
Controversy over Atos is expected to increase next year as the firm begins work on a second £400m contract to assess mobility benefits.
The Scottish Government recently appointed Atos Healthcare to run its staff counselling service in a £720,000 deal, despite backbench SNP opposition.
A spokesman for Glasgow 2014 said: "Glasgow 2014 and our Games Partners would be disappointed if any organisation thought there was an opportunity to detract from this positive and collaborative global celebration for Glasgow and the whole of Scotland.
"We are very proud to have global IT experts Atos as part of Glasgow 2014's sponsor family."
Atos said: "While we fully respect people's right to peaceful protest and understand this is a highly emotive issue, we hope people will view the Games, as we do, as an opportunity to celebrate sporting achievements."