VANCOUVER -- A measure put in place earlier in the COVID-19 pandemic is being walked back by Transport Canada.

BC Ferries was allowing passengers to stay in their cars when parked on enclosed decks as a measure to prevent the spread of novel coronavirus.

But as of the end of the month, passengers will have to leave their vehicles again on most routes.

The service provider said in a statement that the temporary measure will be rescinded by the federal agency as of Sept. 30.

"Enclosed car decks are spaces that represent inherent risk to the travelling public," BC Ferries said in a statement Wednesday.

"During the pandemic these risks were mitigated with additional safety procedures and patrols. However, Transport Canada has now advised BC Ferries that measures have been developed and implemented to prevent the spread of the disease in all transportation modes and businesses across Canada."

Those measures include additional cleaning and sanitation, as well as requiring passengers to wear masks and stay physically distanced from others.

Additionally, BC Ferries will reopen some areas of affected vessels for seating only, including the Pacific Buffet area on Spirit Class ships, to create more space for physical distancing.

No food will be available in the buffet area for now.

BC Ferries' executive director of fleet operations, Darren Johnston, told CTV News this is because it's safer for passengers to be off the car deck.

He said the timing was "entirely" a Transport Canada decision, and that anyone who had questions about the timing should direct them to the federal agency.

"We don't want the public taking out their frustration on our employees on the front line."

Johnston added, however, "Of course we do have concerns about COVID-19. We're still in the middle of a global pandemic, so the timing is interesting."

Premier John Horgan was more direct.

"This is an unwelcome intrusion by the federal government at this time," Horgan said at a news conference in Victoria. "And we're going to pursue it aggressively."

Transport Canada said it's unsafe for passengers to be in an enclosed deck while a vessel is operating due to the difficulties that would arise during an evacuation. The agency also cited the elevated risk of fire when in an enclosed space with fuelled vehicles.

The ministry said worldwide there have been 18 fires between 2005 and 2016 originating from vehicle decks. Five of those fires resulted in major damage, abandonment of the vehicle, injuries or deaths, Transport Canada said in an email to CTV News.

The ministry's director of communications said enclosed decks are built to suppress fires and flooding. They were never built to have people on board, instead being created to contain, not let things or people out.

Graeme Johnston, the provincial president of the BC Ferry & Marine Workers' Union, also weighed in, saying in a statement that "safety is about balancing of risks and COVID-19 tips the scales."

He also added, "We believe the relative risk of people remaining in their vehicles is lower than forcing passengers into already crowded passenger areas."

Reaction from passengers was mixed.

Friends Brenda Zacharias and Brenda Gale from Chilliwack, who were travelling to the Sunshine Coast on a camping trip, both said they thought there should at least be an option to remain in vehicles.

But for Joanne from Langley, it wasn't so clear.

"I've been on a ferry in a storm, in my vehicle, and the front doors (of the ferry) swung open, and let me tell you, you've never seen someone move so fast to get above the deck." she said.

Meanwhile, BC Ferries' Darren Johnston said if anything changes in B.C. to the extent where officials feel they should revisit the ferry policy, there could be a review.

The update will affect the Tsawwassen – Swartz Bay route, as well as sailings between Tsawwassen and Duke Point, and Horseshoe Bay and Departure Bay.

It also affects sailings between Powell River and Comox, and Tsawwassen and the Southern Gulf Islands.

Passengers on those routes will be informed of the regulation if parked on closed car decks. Those on larger vessels who are parked on open, upper decks will be allowed to stay in their vehicles.

Drivers can request being on an upper deck when they check in, and BC Ferries says it will try to accommodate the request when possible, but it may mean waiting for the next sailing in some cases.

In total, 16 ships are affected, Johnston said.

However, those travelling between Horseshoe Bay and Langdale may stay in their vehicles on the lower car decks.

That route is in what Transport Canada refers to as "sheltered" waters, so the stern doors can stay open, effectively making those enclosed decks open.

In a situation where those doors must close, passengers may be asked to leave their vehicles.

The routes between Port Hardy and Prince Rupert, and Prince Rupert and Haida Gwaii, were never subject to the temporary regulation, and therefore remain unchanged.

The update comes a day after B.C. announced a record-breaking caseload of COVID-19. 

Over the long weekend, 429 cases were confirmed in the province, and two more people died of the disease.

With files from CTV News Vancouver's David Molko in Horseshoe Bay.