Several hundred workers demonstrated outside the building before about 250 entered as a council meeting was set to resume on Monday evening.
Papers were strewn about the building and council chamber and a sign calling the mayor a thief was erected during the brief but rowdy protest.
Police, who are also affected by the proposed pension reforms, stood idly by.
Police chief Marc Parent told a news conference today he was disappointed by the turn of events, which has raised questions about the force's ability to do its job.
Municipal employees have been protesting throughout the summer over a provincial government plan to overhaul municipal pensions.
Their actions have ratcheted up in recent days ahead of the beginning of legislature hearings on Bill 3 on Wednesday.
Parent assures there are not two classes of protesters and that charges could be laid after a special group of investigators have looked at evidence and surveillance video.
An examination of policing onsite will also be part of the investigation.
Mayor Denis Coderre denounced the protest as intimidation and bullying tactics and Parent added that police will investigate allegations that protesters threatened some city councillors.