A statement reads "Following a notice from the infrastructure owner, CN Rail, that they are no longer in a position to fulfill their obligations under the Train Service Agreement between VIA Rail and CN Rail, VIA Rail has no other option but to cancel all of its services on the network, effective immediately and until further notice".
The stoppage will also affect passenger trains nationwide, which use CN tracks.
Prime Minister Justin Trudeau and B.C. Premier John Hogan also spoke on Thursday to discuss "how progress on both climate change and reconciliation must continue to be at the forefront of all government actions", as well as how to "work together closely toward a resolution as soon as possible".
Prolonged Indigenous protests blocking key Canadian rail lines could threaten Alberta's economic recovery this year, Premier Jason Kenney said.
"This situation is regrettable for its impact on the economy and on our railroaders as these protests are unrelated to CN's activities, and beyond our control".
The railway said Thursday it was starting a progressive shutdown in the East, while Via Rail cancelled all service on CN tracks in Canada. Thousands have already been forced to find alternative means of travel.
"You need to know we have failed our Indigenous peoples over generations, over centuries".
Along with rail blockades, protesters have blocked politicians in British Columbia from entering the Provincial Legislature and recently blocked Deputy Prime Minister Chrystia Freeland from entering a Halifax City Hall until she was eventually aided by Halifax police.
The C$6bn ($4.5bn, £4bn) project in a remote part of the province about a day's drive from Vancouver has been in the works since 2012.
Some 28% of the pipeline route passes through Wet'suwet'en lands.
Coastal GasLink said it has reached deals with 20 elected indigenous councils along the route to move ahead with construction, including some Wet'suwet'en councils.
Trudeau acknowledged the difficulties the blockades have caused for travellers and businesses, but he made it clear Friday the federal government had no plans to make the RCMP dismantle them.
The letter was in response to a proposal from Stephens and hereditary chiefs of the Wet'suwet'en Nation to meet with provincial and federal ministers to resolve the impasse over the Coastal GasLink pipeline.
Groups including the Grain Growers of Canada, the Forest Products Association of Canada and the Canadian Manufacturers and Exporters have said rail delays are hurting members and the economy. Vancouver Police arrested more than 50 people this week enforcing an injunction order against people blocking access to Vancouver area ports.