Jacques Gagnon, a spokesman for Montreal-based Via Rail, said 26 trains were cancelled on Wednesday, affecting an estimated 5,000 passengers.
Via had to charter about 100 buses to move passengers between Toronto and Ottawa due to the blockade near Napanee in eastern Ontario.
"Due to heavy congestion, affected trains will continue to be replaced by bus service with a return to normal service expected for tomorrow," Via said Wednesday in a release.
Ontario Provincial Police said the blockade began around 9:30 p.m. Tuesday and ended peacefully late Wednesday afternoon.
CN police issued a stop order for all trains going through the area near Kingston, forcing Via Rail to cancel its rail service and bring in buses to get passengers around the blockade.
The blockade was part of recent protests in the Belleville area by a First Nations group calling for a federal inquiry into missing and murdered aboriginal women.
Chief R. Donald Maracle said in a statement Wednesday afternoon that the Tyendinaga Mohawk Council were not involved in the blockade.
"We support the need for a commission of inquiry into this issue but we do not support the blockade," Maracle said.
"It is unfortunate that people feel forced to implement direct action in an effort to draw attention to the issue," he said.
Public Security and Safety Minister Madeleine Meilleur had said it would be up to provincial police to decide if and when to move in to break up the blockade.
Police said they were using a "measured approach that respects everyone's right to peaceful, lawful protest."
The blockade affected Via's Toronto-to-Montreal and Toronto-to-Ottawa service in both directions. Trains between Ottawa and Montreal operated according to the regular schedule.
Gagnon said the blockade situation was expected to cause "substantial expenses," adding that customers with reservations who chose not to travel could receive a full refund.
Demonstrators also temporarily stopped rail traffic in the area earlier this month, leading CN to issue a stop order and Via Rail to cancel trips in the busy Toronto-to-Ottawa corridor.
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