Marine Atlantic says protesters could be banned from the ferry for some time. (CBC)

Small trucking companies remain locked in a battle with Marine Atlantic over the ferry booking system.

Frustrated truckers are threatening to stage protests at the ferry terminals in North Sydney in Nova Scotia and Port aux Basques, in southwestern Newfoundland, which could disrupt ferry service in the Cabot Strait.

They say the new reservation system is resulting in long waits, and that's putting them out of business.

"If Marine Atlantic keeps taking food from our table, we got no other choice. We have to do something," said Chris Howlett, with Akita Equipment, based in Mount Pearl, N.L.

But the Crown corporation has a threat of its own.

Marine Atlantic CEO Wayne Follett sent an email Friday warning truckers that any interruption of service won't be tolerated. He said protesters could be refused service for a period of time.

Tara Laing, spokeswoman for Marine Atlantic, isn't saying much more.

"We've informed people that if there's a disruption in service we would take that very seriously and ask for authorities' help," she said.

Truckers used to board the ferry on a first-come, first-served basis. Since March, they have had to book ahead.

While Marine Atlantic says the new system means fewer and shorter lineups, small trucking companies complain they can't get a reservation because bigger companies are block-booking ahead and cancelling at the last minute.

Howlett said one of his trucks arrived in North Sydney from Ontario on Tuesday, but he couldn't get on the ferry until Aug. 20.

Marine Atlantic 'not fair'

He said Marine Atlantic's email crossed the line.

"It's a federal government agency and, again, we live in a democracy. It's pretty simple. No, it's not fair and I think someone should be doing something about it," Howlett said.

Since the reservation system has been in place, he said, his business has dropped $150,000 from the same period last year.

Dennis Porter, with Porter's Trucking in St. John's, said he supports a protest. He runs fresh produce and fish on eight trucks across Eastern Canada and the eastern U.S. If his cargo isn't delivered on time, it's worthless.

"If we can disrupt the service, maybe if this went national, maybe we could get some attention," he said. "We're going into five months here now. Honestly, truthfully, I won't be around in five more months."

Howlett said truckers are consulting with a lawyer.

Laing said these are the three busiest weeks of the year and there are always delays at this time. She said two new larger ferries will be in service next summer.