The east end pool will be closed for several months after tiles started cracking.
The 2014 venue was due to open within weeks but recent work to strengthen the roof revealed a limited part of the screed below the tiles had separated from the concrete pool tank.
Workers are now in the process of stripping off and replacing the tiles.
Glasgow City Council executive committee heard this will delay the opening for a couple of months.
The swimming venue was closed temporarily last week to allow for preparatory building work.
Operators said the closure was necessary to help the facility prepare for the sporting event, which begins on July 23.
The new 50 metre warm-up pool is open to the public and the 25 metre teaching pool is also open - both will remain open during the retiling work.
Ian Hooper, the Director of Sport and Special Projects at Glasgow Life, said: "We want our facilities to look at their absolute best during the Games and having a newly tiled competition pool will see Tollcross shine.
"By completing this work now, while contractors are on site, we will also avoid having to close the pool at a future date, which helps to minimise disruption.
"The new six-lane 50 metre warm-up pool, the 25 metre teaching pool and the rest of the facility will remain open to the public throughout."
It is expected that the work to retile the pool will be completed by late March.In May 2013, the swim centre reopened after a £14million upgrade, which took 19 months to complete.
The work resulted in an improved 10-lane, 50m competition pool, a new six-lane, 50m warm-up pool and an extra 1000 permanent seats, creating one of the largest facilities of its kind in Europe.
On October 17, the pools closed again, so a wall could be moved to allow temporary seating to be installed in time for the Commonwealth Games.
Part of the centre's roof also had to be strengthened.