The anticipated costs of the riverside landmark on the banks of the Clyde ( pictured) have risen from initial estimates of £50.5 million to almost £60 million.
According to Glasgow City Council, the hike is due to the increased cost of the 'roofing structure', which has been designed to 'hide all of the plant' from public display.
However, a council spokesman also claimed the original budget had been set before Hadid's appointment and that the new estimate is not expected to 'significantly alter' as the project moves towards completion in 2008.
He said: 'What we had at the start of the project was a very early estimate and this is now a fully costed project.
'This council has a good record of delivering on budget and on time once a scheme has been costed - and we are not expecting any significant alteration to that.'
He added: 'We believe the museum will absolutely be the jewel in the crown of the Clyde regeneration.'
Hadid has faced numerous controversies over spiralling budgets over the past few months, with costs at her Architecture Foundation building in south London increasing dramatically ( Cost rises as plans for Zaha's Architecture Foundation building swell) and her plans for the 2012 Olympic Aquatic Centre being sent back to the drawing board after the proposals came in at nearly twice the budget ( Zaha forced back to drawing board as Olympic pool costs spiral).
Hadid was unavailable for comment over the most recent controversy.