"It is with deep sadness that I have reason to believe that a Canadian citizen, Robert Hall, held hostage in the Philippines since September 21, 2015, has been killed by his captors," Trudeau said in a statement.
Members of the notorious kidnap-for-ransom Abu Sayyaf gang had said they would murder Hall if they did not receive 300 million pesos (USD 6.5 million) ransom by today.
"While Canadian officials are working closely with authorities in the Philippines to formally confirm Hall's death, we have compelling reason to believe that reports to this effect are, unfortunately, true," Trudeau said.
Hall was among four people abducted in September last year from aboard yachts at a tourist resort in the southern Philippines.
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Another Canadian who was abducted at the same time, John Ridsdel, was beheaded in April after a similar ransom demand of 300 million pesos was not paid.
In the Philippines, authorities would not confirm Hall had been killed.
"No formal report has reached me. I cannot confirm that," regional military spokesman Major Filemon Tan told AFP.
Listed by the United States as a terrorist organisation, the Abu Sayyaf is a loose network of Islamic militants that was founded in the early 1990s with money from Osama bin Laden's Al-Qaeda network.
It is regarded as one of the most radical offshoots of a Muslim separatist insurgency in the south of the mainly Catholic Philippines that has claimed more than 100,000 lives since the 1970s.
The Abu Sayyaf is believed to have just a few hundred armed followers but authorities regard it is as one of the most dangerous terrorist groups in the Philippines.