Via Rail says it expects the disruptions on the Toronto to Montreal and Toronto to Ottawa routes to continue well into Friday morning.
The company says in a tweet that morning trains 41, 43, 51, 61, 50 and 60 will be replaced by bus.
The disruptions follow the derailment of a C-N freight train near Brockville, Ontario.
A C-N spokeswoman says no one was injured when the 26-car eastbound freight train derailed about 4 a-m.
Via says about 36-hundred passengers were affected by the derailment.
Spokeswoman Mylene Belanger says Via has secured buses for the rest of today to transport the remaining passengers.
Meanwhile, C-N says in a tweet that it hopes to have one line open late today or early tomorrow.