An alert about 8.15am advised clearance had since been received to continue services, but that passengers should expect delays.
One passenger, who did not want to be named, said he was on the train this morning when the service was stopped.
“It was announced that there are trespassers in the tunnel,” he said.
“Trains are running between Waikanae and Porirua and back again. Lots of folks will [work from home] if they can.”
The man said the train manager did “an excellent job” with the little information he had.
“At least no one has been killed,” he added.
The impact of the cancellations is hitting other commuters, with those who would normally be catching the buses getting left out in the cold.
One woman trying to travel in from Johnsonville said at least two buses she was trying to catch had skipped her bus stop, driving past with full loads of travellers.
Metlink has been contacted for comment.