The operators of Tollcross International Swimming Centre said the closure is necessary to help the facility prepare for the sporting event, which begins on July 23.
But sources close to the major championship, which was due to take place on January 25, said they had been told the centre required renovation work.
It is understood organisers had been looking at other venues including Dollan Baths in East Kilbride to reschedule in March as there were doubts about whether Tollcross would be available.
But Glasgow Life, which operates the facility, said the booking was unconfirmed because they knew there was preparatory "building work" scheduled and denied there were problems with the roof.
The main pool, which shut last month, is expected to be reopened in February. Glasgow Life has written to the championship's organisers, the Scottish Schools Swimming Association, to reschedule but had no response.
A Glasgow Life spokesman said "substantial work" was required including removing a wall to put in temporary seating and work to ensure overhead TV cameras can be installed in the roof.
The new centre was open to the public in May after a 19-month refurbishment costing £13.8 million.
It was revamped into a 10-lane, 50-metre competition pool and a completely new six-lane 50m warm-up pool.
An extra 1000 permanent seats were added to the 1000 in place before the revamp started in October 2011.
At the time Glasgow Life said a further 3000 temporary seats will be in place during the Games.
But its closure, described as "unexpected" in school circulars, has led to the postponement of the January 25 championships.
A championships source said he was "surprised" by Glasgow Life's response adding: "They would say it was expected work. They closed it.
"There was something structural wrong with the roof and they needed to fix that before the Commonwealth Games.
"And there are no other pools available. Getting a pool is not easy."
Tollcross was to host the 2014 swimming competition and the 2015 IPC World Swimming Championships.
The venue is also an integral part of Glasgow's bid to host the 2018 Youth Olympic Games.
The venue will also operate as a community sports facility and features an enlarged fitness suite.
A spokesman for Glasgow Life said: "As part of our preparations for the Commonwealth Games, a series of planned works led to the temporary closure of the pool, although the rest of the facility remains open.
"The 50-metre warm-up pool will reopen to the public on Monday, with the main pool reopening next month.
"To minimise disruption, we alerted the event organisers that there may be a slight delay in reopening and have been working with them to find another date to host the championships, or an alternative facility."