Trudeau says it's now theoretically possible the trash could be repatriated by Canada, although there's still questions around who will pay for it.
"This is a tremendous concern to Canada and to many, many countries around the world", he said.
Speaking to reporters in Manila, Trudeau says the issue is a long-standing irritant rooted in a commercial transaction that didn't involve government.
Trudeau was apparently one of the only leaders at a regional summit in Manila to bring up the issue, expressing his concern over extrajudicial killings in the Philippines in talks with Duterte.
Prime Minister Justin Trudeau directly raised human-rights concerns with Rodrigo Duterte - including extrajudicial killings carried out by security forces in his country - in a confrontation Tuesday that the Philippine president later derided as a "personal and official insult".
Duterte also threatened to ban at least 2 United States lawmakers from entering the Philippines after they raised concerns about possible human rights violations committed under his drug war.
Duterte has drawn criticism from global groups and foreign governments over his bloody crackdown on illegal drugs.
"I will not answer to any other bullshit, especially to foreigners, " he said.
"That is why you hear me throwing down epithets and curses, 'bullsh*t, ' because it angers me", he added.
Duterte chairs world leaders as the Philippines holds the rotating chair of the 10-nation ASEAN group.
"I actually had an opportunity to have a conversation with President Duterte just before our meeting earlier this morning, in which I emphasized, of course, the people-to-people ties between Canada and the Philippines and the great connections there", said Trudeau.
"The president was receptive to my comments and it was throughout a very cordial and positive exchange, " he said.
"Canada has earned a reputation for being able to have frank, firm discussions around rule of law and human rights with partners around the world".
In 2014, the Philippine government recommended the containers be returned to Canada under the provisions of the Basel Convention, which prohibits developed countries from shipping waste to developing nations.
The two sides later issued a statement saying they "underscored that human rights and the dignity of human life are essential, and agreed to continue mainstreaming the human rights agenda in their national programs".
According to Trudeau, it is important to talk about human rights, even admitting that Canada has its own share of instances where some of its citizens get neglected or marginalized.