HMCS Preserver was fuelling at a refinery when an improper seal allowed fuel to seep into the pipe, which carries solid waste, and then flow into the harbour, the report says.
The navy was able to recover most of the fuel before it spread to shore or cause extensive damage.
The report dated March 29, 2011 — about two weeks after the spill — was obtained through access-to-information legislation. A final report hasn't been completed.
Irving Shipbuilding was contracted by the navy to carry out an inspection of the 41-year-old supply vessel's drainage lines in September 2010. It found sections of the pipe were "deteriorated and required replacement," says the report.
Irving was then hired to replace the pipes and install new fasteners and gaskets. But navy staff weren't given the opportunity to inspect those repairs, the report says.
"National Defence quality assurance representative staff had responsibility to verify that these repairs were done correctly," says the report.
"This did not happen for a myriad of reasons which will be determined over the course of the investigation."
The report says the lead investigator should find out why the drain line was not tested by Irving and the navy.
Mary Keith, a spokeswoman for Irving Shipbuilding, declined to be interviewed but in an email said the company hadn't seen the report.
"We are not aware of a report, nor were we invited to participate, and therefore are not able to comment," she said.
"Our commitment has and continues to be the provision of quality service to the navy in the building and repair of vessels."
Cmdr. Larry Jones, the commander of HMCS Preserver, said the navy has inspected other drainage lines on the ship to ensure there isn't another leak.
"When you discover one technical issue, then you ensure that all of your other systems are sound," he said in a phone interview.
"My ship's staff have done a complete investigation of all the other systems, particularly with regard to fuel systems to ensure there are no other irregularities."
Jones wasn't the ship's commander at the time of the leak and said he couldn't comment on the report's findings, but he believes the problem won't occur again.
Maj. Paul Doucette, a spokesman for the Defence Department, also declined to comment on the report.
In his report, Lt.-Col. J.F. Sangster says he will provide recommendations about the ship's drainage system in the short-term, as well as more long-term solutions for the aging supply vessels.
In a separate email sent March 17, 2011, the day after the leak, a senior navy engineer raised concerns with other officers about the aging vessels.
Cmdr. R.W. Jones said for 10 years, the designs and diagrams that outline systems such as the drainage lines aboard HMCS Preserver and its sister ship, HMCS Protecteur, had not been as well maintained as the records on other navy ships.
"The decision was very deliberate, given that 10 years ago we were all expecting Preserver and Protecteur to be razor blades by now," he said in the email, which was also obtained through access-to-information legislation.
"The technical drawings now have gaps/inconsistencies."