A leaking radiator on the fourth floor caused dirty water to pour from a councillor's office down into the basement.
Some rooms were left in about two inches of water and the famous Satinwood Suite – which is lined with the now extinct exotic satinwood imported from Queensland, Australia – could be closed for up to six weeks.
Various events scheduled in the building for the next few weeks, including a Scottish Women In Business conference and a Strathclyde Police Authority meeting, will have to be relocated.
Council workmen and specialist restoration workers have been conducting a massive clean-up in the aftermath.
The damage was discovered by security staff who found the water running down the 125-year-old building's internal walls at about 2.30am on Monday.
Keith Dalkin, manager of the City Chambers, said it was too early to say how much it would cost to repair the damage, but it was expected to exceed thousands of pounds.
He said: "It will take between five and six weeks for the walls and floors to dry out. Because of the age of the building we have to let it dry very slowly."
The City Chambers was opened in 1888 by Queen Victoria and is regarded as one of the city's finest buildings.