The council received a report from Police Scotland that the statue had disappeared from Edmiston Drive today at around 9am - and they believe it has been stolen.
The statues across the city have also been subjected to vandalism with plaques or QR codes defaced.
The local authority had intended to leave the statues across the 25 location in the city until the end of the school holidays - but now they have been forced to take action and remove them.
A spokesman for Glasgow City Council said: "In recent days, there have been incidents of vandalism to some of the Clydes along the trail, including defacement of the plaques and QR codes, which are there to help people complete the trail using the Clyde's Trail smartphone app.
"It was our intention for the Clydes to remain in their current locations and for the trail to be enjoyed until the end of the school holidays. Thereafter, we planned to take each of the statues in from Sunday, August 17 to clean them up and carry out any routine maintenance required.
"However, to ensure the safety of the remaining Clydes, we have decided to begin removing them from today.
"During this process, discussions will continue regarding the long-term home for the Clyde statues, including the wooden Clyde in Queen's Park and the floral Clydes at Glasgow Green and Kelvingrove Art Gallery and Museum.
"It is, and has always been, our plan that Clyde will remain on show in the city, providing a lasting legacy of Glasgow's Games that will live on and be enjoyed by residents and visitors."
Clyde's Trail is made up of 25 unique, life-sized fibreglass statues of the Glasgow 2014 Commonwealth Games mascot, which are on display at locations across the city.
Children and young people were asked to come up with a range of outfits for Clyde as part of a legacy project run earlier this year by Glasgow City Council and Glasgow 2014 in partnership with children's charity UNICEF.
Pupils from Glasgow's nurseries, primary and secondary schools were invited to submit designs inspired by the city itself. Nearly 200 entries were received with themes reflecting iconic landmarks, architecture and people, such as the River Clyde, the SSE Hydro and Charles Rennie Mackintosh. The 25 brightly-painted sculptures were then brought to life by Wild in Art using local and national artists.
Clyde's Trail was a key centrepiece in a programme of activity by Glasgow City Council to dress Glasgow for the Games - aimed at creating a vibrant, fun and inspiring environment for residents, visitors, spectators, athletes and the world's media.
Clyde has become synonymous with Glasgow's Games and the trail has proved massively popular, with tens of thousands of fans queuing to have their picture taken beside Clyde across the city in recent weeks.
Throughout the Games there were some instances of Clyde being 'accessorised' - with flags, scarves, hats and stickers - however, the council wanted people to find him as the children who designed each outfit intended, and any items that were added to the children's artwork were removed as part of the daily maintenance programme.
The Evening Times also reported that a petition has been launched to make Clyde the city's official mascot.