Via, which uses the same tracks, was forced to cancel all its trains between Toronto and Montreal and Toronto and Ottawa Saturday in both directions, affecting some 1,500 passengers.
A Via official said in an email some 700 people were on trains that were halted as a result of the CN derailment near Bowmanville and were taken to their destinations using alternate means.
A spokesman for CN said that seven cars of a westbound CN train derailed Saturday afternoon, but Brent Kossey said no injuries were reported and no dangerous goods were involved in the derailment.
He said the cause of the derailment is currently under investigation.
Via says full service was expected to resume Sunday.
The rail company said service between Montreal and Ottawa was not affected.