Workers installed the famous symbol in George Square in preparation for the arrival of the Olympic torch in less than two weeks but they were covered up as visitors looked on.
The Scottish leg of the torch relay will begin in Glasgow on June 8, when singer-songwriter Eliza Doolittle, Scots Brit Award winner Emeli Sande and indie rockers General Fiasco will perform at a free concert in the Square.
From there the flame will be carried to Inverness, Shetland, Orkney and the Isle of Lewis.
Meanwhile, Olympic organisers have been criticised for a "completely ridiculous" ban on the Saltire being flown during the Games over Scotland's national stadium, where some Olympic football matches will be played.
Under Olympic rules, Scottish athletes represent Great Britain, meaning only the Union flag should officially be flown at venues.
Alyn Smith, an SNP member of the European Parliament, has complained to Lord Coe, chairman of the London 2012 organising committee.
Mr Smith said: "The Saltire normally flies above Hampden 365 days of the year. Forcing it to be taken down will not only anger many home-based supporters, but also disrespects our nationhood."
Terms and conditions on tickets state there should be no flags of countries that are not participating.
A London 2012 spokesman later said: "There is no question of the Scottish flag being banned. Spectators are welcome to bring flags in, as long as they meet the size requirements set out in our terms and conditions. In terms of the flag flying from the stadium, we are clarifying the situation."