Canadian immigration officials have begun processing some 490 migrants, thought to be Tamils from Sri Lanka who have spent three months at sea.
Officials say they want to establish whether any of them are militants from the Tamil Tiger group, which Canada regards as a terrorist organisation.
The Tamils' ship reached Canadian waters on Friday and was escorted to a British Columbia navy base.
Dozens of border officials were waiting to remove those on board from the ship.
Sri Lanka's civil war ended in crushing defeat for the Tamil Tigers last year, but many Tamils say they still suffer discrimination and repression from the government.
Canada, which is home to around 300,000 Tamils, will not accept Tamil Tigers as migrants or refugees.
Authorities intercepted the ship, the MV Sun Sea, off British Columbia. It had reportedly crossed the Pacific after being turned away from Australia.
Canadian Public Safety Minister Vic Toews said the vessel had declared it had 490 refugees on board, but he said some were "suspected human smugglers and terrorists".
Despite having spent so long at sea, there were no reports of any serious injuries or illnesses.
Gary Anandasangaree, a lawyer with the Canadian Tamil Congress, expressed surprise at the size of the ship - which measures 194ft (59m) - given the number of passengers.
"It clearly gives us an idea of the type of conditions that could have been inside. Very cramped, given the size," Mr Anandasangaree said.
There are unconfirmed reports that children were on board.
War's violent end
The Tamil Tiger rebels were defeated by the Sri Lankan army last year after more than two decades of conflict.
The rebels were accused of using child soldiers, suicide bombers and human shields.
But government forces were criticised over the bloody end to the war, in which many Tamils were killed and tens of thousands were rounded up into camps.
Sri Lanka's high commissioner to Canada, Chitranganee Wagiswara, has urged Canada to refuse the asylum claims of the MV Sun Sea passengers.
She says the ship is part of a people-trafficking operation linked to the Tamil Tigers.
Toronto-based immigration lawyer Lorne Waldman told the Canadian Broadcasting Corporation (CBC) that the country had "no choice" but to take the people in.
"Once they're here, we can determine what we'll ultimately do with them," he said.
Last October, a ship carrying 76 Sri Lankan migrants was intercepted in Canadian waters after crossing the Pacific.
All of the men were immediately detained in jails around the Vancouver area, but all apart from one were released shortly afterwards.
Some of those on board said they had paid thousands of dollars for a berth.