Opposition politicians and environmental organisations have managed to put a temporary stop to the restoration work after applying to Milan's regional administrative tribunal, says the Guardian newspaper in the UK.
They fear the building work does not follow the original plans approved by Milan city council.
Dancer Carla Fracci, who has performed many times on the stage, has spoken out about her concerns about the acoustics of the revamped venue and its appearance.
The 18th Century venue is undergoing a radical restoration programme at a cost of £25m and will remain closed to the public for more than two years.
But the plans for its future have not gone down well in some circles.
Alarm
Ms Fracci and the former chairman of state broadcaster RAI, Roberto Zaccaria, told a press conference the city council had not given proper approval to the project.
"They have even destroyed the orchestra pit. I raised the alarm a year ago but they would not listen," said Ms Fracci.
The group has also voiced concerns about the way the work was tendered.
Milly Moratti, a Green party councillor in Milan, is angry the theatre's stage and backstage area had not been preserved for future display in a museum.
Improved
A television programme exposed how dramatic the renovation, with pictures of bulldozers at work and gaping hole where the backstage had been were secretly filmed.
But La Scala bosses maintain the staging area has been maintained for future exhibits.
The Guardian quotes a council spokeswoman who said the appearance of the opera house would remain unchanged and the acoustics would be improved not worsened.
La Scala's officials say the restoration is necessary for the company to put on more and better productions.
Performances are being held at the Arcimboldi theatre until work is completed in late 2004.