The council's £823,000 new fountains in Exchange Square have been turned off for 'routine maintenance' - just two days after they were unveiled to the public.
Specialist contractors were back on site and two thirds of the feature was not in use when the Manchester Evening News visited on Wednesday afternoon.
There was no water running, various parts of the fountains had been pulled apart, and two members of staff from Glossop-based firm the Fountain Company were carrying out work.
A council spokesman described what was going as 'routine maintenance' as a result of the water feature being turned on.
'Gunk' from the construction process needs to be full cleared out the system, it is understood.
"This is not unexpected and is all part of the process," the spokesman said.
"Work on two of the three sections has already been completed for today and the third one should be finished shortly, at which point, the feature will be switched back on."
The water feature was officially opened on Monday following a major revamp that took almost a year to complete.
Council bosses originally signed off £700,000 for the project and said it was expected to take around six months.
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But the redesign ended up going over budget by more than £120,000 and delayed by five months due to 'technical issues'.
It is understood this centred on the original granite slates which were found to have cracks and plans had to be revised.
The fountains were originally built 20 years ago as part of the overhaul of the Exchange Square area following the IRA bomb in 1996.
Council bosses said they was in need of sprucing up, although the bulk of the money was spent on mechanical repairs, similar to those carried out in Piccadilly Gardens at a cost of £400,000.
In a press release, the council said the redesign 'pays homage' to the original feature 'while improving its energy-efficiency and increasing its resilience to damage'.
The fountains, opposite the Corn Exchange, are now lit with colour-changing, energy-efficient LED lighting and animated with water jets that continually run through a 15-minute 'chase, dance and wave sequence' between 7am and 11pm.
The taps at the top of the water feature have also been retained and restored.
Sections of the original slate stepping stones have been retained, the council added, but have been 'inlaid and bonded into three raised plinths and set within a surrounding of granite, inviting visitors to sit and enjoy the animation of the water and the lighting'.
It is hoped the new design will minimise levels of debris entering the filter system and reduce the damage caused to the original stepping stones as a result of people walking over the feature.
New pumps and filters have also been installed which the council says will save energy and reduce the need for ongoing maintenance.
The feature was designed and installed by Cruden Property Services and the Fountain Company (Glossop), who also designed and installed the St Peter’s Square water feature.
The expenditure immediately sparked criticism from some M.E.N readers and the opposition Lib Dems.
Councillor Richard Kilpatrick said: "In the last few of years, Labour have wasted £1.2m on failing fountains.
"That’s enough to house every single person sleeping rough in Manchester for an entire year, along with a hot meal, a warm shower and access to a support worker.
"These stupid fountains are a constant reminder of this Council's breathtaking incompetence, and just how often and wrong their priorities are.
"As we head into the elections this year, Lib Dems will fight to re-prioritise public money to end homelessness and invest in our public services – not vanity projects and 'dancing' failing fountains."
However, ruling Labour councillors said the fountains refurbishment had been a worthwhile investment.
Councillor Angeliki Stogia, the council’s Executive Member for the Environment, Planning and Transport, said: "Exchange Square is a great public space and has long been a focal point for local businesses, events and visitors.
"The attractive water feature has always been a big part of what makes it stand out and this revamp will help to secure its long-term future.
"This investment in the look and feel of the Square will help it to continue to serve Mancunians and our many visitors from around the globe, acting as a thriving place where people enjoy spending their time and a key hub of economic activity, supporting thousands of city centre jobs.
"I'd like to thank CityCo for supporting this scheme and local businesses for their patience while the work was carried out."
