Staff took 4261 sick days during the 17 days of the Games – an increase of 443 on the same dates last year when they took 3818 sick days.
The leaves of absence were taken by staff among the 19,252 workers directly employed by the council, such as teachers, office personnel, press officers and executives, between the opening ceremony on July 27 and the close of the Games on August 12.
The worst offenders were in the social work department, whose 4345 staff took 2311 days.
The same department last year took 1944 sick days, nearly 300 fewer.
The figures were slammed by Jonathan Isaby, of the campaign group TaxpayerScotland.
He said: "The number of sick days taken by public sector staff is already systematically higher than it is in the private sector, and this increase during the Olympics will have cost families in Glasgow dear.
"It is simply not fair that taxpayers keep having to pick up the bill for excessive sick leave at their local council.
"If there is any evidence that any of those who took sick days during the Olympics were not genuinely sick, the council must crack down hard on such behaviour and make an example of any staff who skipped work."
The second highest number of sick days came from the land and environmental services department, who took 1048 days off sick against 745 in 2011.
The only departments that didn't see an increase were education and financial.
Education workers took 414 sick days during the Games – it was 518 last year.
Financial services staff took 208 days, against 251.5 in 2011.
The fewest number of sick days were taken by 925 staff in the chief executive and corporate services departments. They took 182 – 80 less than last year.
The figures were revealed through the Freedom Of Information Act and come just a week after it was revealed workers at the council take an average of 14 days sick leave every year, three times that of the private sector.
A council spokesman said: "There is no evidence to link the absence rates with the Olympics.
"Our absence figures have more than halved over the last few years and we have saved £17million for council tax payers as a result.
"We have robust measures in place to manage sickness absence, which includes disciplinary action where appropriate."