The migrants repeatedly attempted to get inside the trailers and illegally enter the UK, according to Calais port authorities.
The VIIA Britanica railway has halted its operations until September. The shutdown comes just a few months after the rail motorway began operations.
It has been mainly used to transport trailers, allowing the goods to cross France in 22 hours, avoiding a much longer 1,200-kilometer (745-mile) commute via roads.
Port authorities said in a statement that motorway services have been halted after a “resurgence in migrant intrusions in past weeks.”
“The situation keeps getting worse. We don’t know what to do anymore to be heard. The migrants, some of whom are armed, climb into the trailers, they rip the tarpaulins,” said Antoine Ravisse, one of the protesters against the Calais migrant crisis.
“Our clients lose confidence in us, sometimes their merchandise is destroyed. The cost is enormous,” Ravisse added.
Once the loaded trailers reach the French port of Calais from Spain, they are left unsupervised before being loaded onto ferries to cross the English Channel.
Each train that comes to Calais can carry up to 40 trailers, giving migrants plenty of opportunity.
Following the rail motorway shutdown, Calais port employees organized a go-slow on a highway protest.
There are still around 4,500 migrants living in the Jungle camp even after the French government tried to dismantle the illegally built huts back in March.
Media focus has been zeroed in on the camp. The local government has promised to bulldoze the rest of the camp.
Most of the residents there are migrants from war-torn countries in North Africa and the Middle East.
In the most recent comments, the Calais mayor, Natacha Bouchart, said the date for demolition will be set soon.
“It is absolutely urgent for this town, its people and its businesses,” she said on Monday. “We can’t wait any longer. We need to know as soon as possible how and when the Jungle will be torn down.”