Transport Canada spokeswoman Yvette Myers said investigators have also found another unrelated problem on the MV Marathassa contributed to the spill but declined to provide details because of an ongoing investigation.
Hours after her update, the B.C. government came under fire from New Democrats over the federal response to the spill that started on Wednesday night and continued overnight.
Myers told a news conference Monday that problems arose in a section of the ship, known as a duct keel, which is a tunnel that runs along the centre line of a vessel and carries pipes.
"We have found evidence of some mechanical problems with pumping, with some of the valves and the piping system," she said. "This caused the oil to leak into the duct keel."
On its own, she said, the leak would have only caused a "mess" in the ship's hull and the fuel would not have gone anywhere without the unrelated issue that investigators discovered.
The bunker fuel that gushed out soiled several beaches along English Bay and Burrard Inlet.
Canadian Coast Guard commissioner Jody Thomas said 80 per cent of the estimated spill had been cleaned up by Thursday and what's left is "a negligible amount."
She said the cleanup of the spill has cost "a lot of money" and will be the responsibility of the ship's owners, but she declined to provide an estimate.
Environment Canada spokesman Owen Rusticus said the estimated 2,700 litres of fuel is based on the observations of investigators who flew above the spill.
He said a plane sensor mapped the extent of the spill on the water, and crew members observed it.
"The 2,700-litre estimate is a conservative estimate that is based on the thickness of the oil in combination with its appearance on the surface, and then the actual area," Rusticus said.
Myers said it could take several days or even a week to determine how much fuel spilled.
Investigators will calculate how much fuel the MV Marathassa carried when it left Japan, how much it burned en route to Vancouver, how much was located in the duct keel and how much likely evaporated.
"The vessel owners and the crew are co-operating fully with our investigation," she said.
Opposition NDP Leader John Horgan said in the B.C. legislature Monday that the Liberal government should demand that the federal government defend B.C.'s coast, just as they defend Canada's East Coast.
New Democrat Spencer Chandra Herbert, who represents Vancouver's West End, said his constituents can't use the beaches because of the spill.
"When will there be action?" he said. "When will this government actually do more than just talk and wag their finger?"
Environment Minister Mary Polak said the Canadian Coast Guard showed no leadership at the start of the crisis, but the federal agency has stepped up after the province made repeated requests.
"The response to this spill was unacceptable," she said. "It was not world class."
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