Notices of non-compliance were sent to MM&A after inspectors carried out safety checks on six sections of the rail line, located between Saint-Jean-sur-Richelieu and Lac-Mégantic.
According to the report, the condition of the rails raised concerns about safety.
Railway ties were found to be "fair" or "substandard" in many places, and several crossings raised concerns because of poor surface conditions, signage and sightlines.
Transport Canada said some sections of the track could not even be inspected because they were overgrown with vegetation.
The inspections were conducted two weeks after the train derailment and explosion in Lac-Mégantic that killed 47 people.
Allen Hamel, a Quebec train safety expert, said the non-compliance notices do not necessarily mean the tracks are unsafe, but are meant as a corrective measure.
He says not applying the necessary corrections could lead to serious fines, and the rail line being shut down.
"They must absolutely correct the points on non-compliance," said Hamel.
Transport Canada says it is most concerned about one section where a concentration of defective ties was found near a propane storage facility.
MM&A could not be reached for comment.Suggest a correction