The passengers on the Toronto to Montreal and Toronto to Ottawa routes are being transported around the site of the derailment by bus.
"Delays may be expected, between 30 minutes and two hours depending on the situation," said spokeswoman Mylene Belanger.
Lindsay Fedchyshyn, a CN spokeswoman, says no one was injured when the 26-car eastbound freight train derailed near the eastern Ontario city at about 4 a.m. Thursday.
The freight train included two loaded automobile carriers and had five cars carrying carbon powder and 13 unloaded fuel tank cars, she said.
The route was expected to be blocked at least for the morning and the site was being assessed for any possible leaks, Fedchyshyn said.
The Transportation Safety Board of Canada has also sent a team of investigators to the site.
Jacques Gagnon, another Via Rail spokesman, said it can be difficult to find buses to transport passengers during the summer peak vacation season when charter buses are in high demand.
But the company has managed to secure enough buses to maintain service until the cleanup is done, he said, calling the situation "a logistic challenge."
"I understand there's a lineup of freight trains that cannot go through as a result of the derailment," he added.