The allegations include delayed repairs, sloppy welding work and a failure to report key issues to the regulator, Reuters reported.
NEB is reportedly reviewing an allegation that TransCanada delayed pipeline damage repair caused by a construction crew in May 2013 about 150km north of Calgary, and also failed to report it to the regulator.
Another allegation mentions about poor repair work done to the North Central Corridor, which serves companies in the oil sands. This natural gas pipeline was damaged following an October 2013 explosion near Wabasca, Alberta.
The investigation has been initiated after a whistleblower employee of the company complained about the loopholes.
TransCanada did not reveal any details but accepted that an internal probe is on after someone previously raised them within the company, the news agency said.
TransCanada spokesman Davis Sheremata told Reuters that TransCanada was working diligently to gather relevant information to share with the regulator, but that it did not see any of the allegations representing either an immediate or long term threat to the public or its assets.
"We make it clear to all of our staff and contractors that we will not tolerate anything that undermines the safety and reliability of our facilities," he said.
This is the second time that the NEB is investigating into the safety code violations by the company.
Canada’s second-largest pipeline company previously faced a similar situation when allegations were publicly made by a former employee in 2012.
