The shut down comes just days after a computer glitch almost scuppered the entire system on Thursday. The problem took almost an hour to be resolved, leaving the evening rush hour in chaos.
Monday's shut down was described as a "technical issue" by TransLink.
"Due to a technical issue at Skytrain, there are significant delays impacting the Expo & Millennium Line trains. It is also impacting our ability to communicate to passengers in train cars or platforms," says the TransLink website.
"We are working hard to resolve this issue. For those passengers in the trains, please stay in the cars until instructed. Thank-you for your patience."
An image posted to Twitter shows a number of passengers walking along the tracks next to a stopped train.