The Transport Department hasn't established an effective monitoring program to ensure rail companies are being properly audited to ensure security issues are corrected quickly, the Transportation Safety Board said in a statement.
The board, which investigates transport accidents and makes recommendations for improvement, said auditing measures are lacking even though the federal department has introduced "multiple layers of defences" to prevent runaway trains.
A Montreal, Maine & Atlantic Railway (MMA) train hauling tanker cars loaded with volatile crude oil broke loose and barrelled into Lac-Megantic on July 6, 2013, before derailing and exploding.
The tragedy claimed the lives of 47 people and wiped out a large swath of the downtown area.
"The minister of transport and the department have taken strong action to improve rail safety in the wake of the Lac-Megantic tragedy, but more work needs to be done,” said TSB chair Kathy Fox.
"Canadians deserve no less than the safest transportation system."
The federal agency issued a report last August that identified 18 key factors it says led to the Quebec catastrophe, including a lack of government oversight and a penny-pinching railway.
It said Wednesday that while there has been significant progress, it only considers the response "satisfactory, in part," and adds the government "has not yet demonstrated that it has implemented an effective oversight regime to ensure all railways will be adequately audited."
Transport Canada has committed to implementing new rules and strengthening its ability to enforce them through the hiring of additional auditors and improved training of current staff.
In Ottawa, Transport Minister Lisa Raitt said jobs specifically dealing with oversight have been posted and there is a concerted effort by the government to fill them.
Raitt said she takes all TSB recommendations seriously and the department is working hard to ensure they are fulfilled.
"Safety oversight is incredibly important," she said. "The department knows they have to work on this, they'll continue to work on it."