Students and staff from École Baril moved into the École Louis-Riel building in mid-October.
In a notice obtained by Radio-Canada, Montreal's public health department urges the school board to rectify the situation.
According to the notice, the ventilation system in the current building has not been cleaned since the school was first built in 1973.
In 2011, students and staff from the school were moved temporarily to another location, École Hochelaga, due to mould problems at their original location. The same issues were later found in the Hochelaga facility, forcing them to relocate again.
Several people have had their health problems return since they moved to the Louis-Riel space, likely a result of contaminants in the air, according to Dr. Jacques Alain, of the public health department.
Alain also said it's possible students may also be suffering from exposure to the poor air quality.
Montreal's health department got involved in the case in December after they visited the site and received a report on the ventilation system they said was dated April, 2012.
According to the health department, they did not receive the report until the end of December, long after the students and staff had been transferred to the Louis-Riel location.
The health department says it would not have given the school board approval for the new space in October if it had been aware of the air conditions.
But Daniel Duranleau, president of the Commission scolaire de Montréal (CSDM) said the report should not come as a surprise.
"The question of the ventilation system and the fact that it had dust inside it: these facts have been established. This is nothing new," he said.
The cleaning of the ventilation system, which began on Monday, is expected to last two months at a cost of $200,000. Officials say it should be enough to rectify the problem.
The school will remain open while the cleaning takes place.
As the staff and students deal with air quality issues in their latest of three locations, repair work on the original École Baril is on hold.
The CSDM, having invested $4 million in the school, is waiting for instructions from the ministry of education before it can proceed.