Officials discovered the breach while investigating the explosion at Neptune Technologies and Bio Resources.
The Nov. 8 blast and resulting fire killed three people and injured 18 others.
A tank of acetone, which is a highly flammable solvent, is believed to have been the source.
According to information obtained by Radio-Canada, the quantity of acetone inside the factory was higher than the amount authorized by the ministry.
In 2002, the Ministry of Environment authorized Neptune Technologies to keep 33,000 litres of acetone outside the factory and 6,000 litres inside.
Investigators have found that the quantity of acetone was much higher, according to Radio-Canada.
Environment Quebec officials estimated that 15,000 litres of acetone was burned in the fire that followed the explosion.
Investigators also discovered other reservoirs in the rubble, with a total capacity of 27,000 litres.
Lise Vaillancourt, a senior official with Quebec's Environment Ministry, said officials aren't yet sure exactly how much surplus acetone was being stored at the facilities.
Vaillancourt said that notices of non-compliance have been sent to the company.
The Ministry will look into what action it can take under the Environmental Quality Act to deal with the breach of standards.
Factory began expansion without authorization
Neptune Technologies had also begun to expand the capacity of its factory.
According to Radio-Canada, the expansion was not authorized by the ministry. Vaillancourt said she met with the director of Neptune Technologies earlier this year and they discussed the fact that specific standards must be met before the work could begin.
Despite not gaining ministry approval, Neptune Technologies obtained $3,000,000 from Quebec at the beginning of 2012 to fund an expansion of the factory.
A spokesperson for Neptune Technologies said Friday that the company has nothing to hide and will cooperate with the investigation.
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