Canada is being urged to retrieve 103 shipping containers sent in 2013 and 2014 that allegedly contain toxic waste.
The Canadian authorities have said they have no authority to compel a private shipping firm to retrieve the shipment.
The Philippines first raised the issue with Canada in 2014. Duterte was elected in 2016.
In 2017 Prime Minister Justin Trudeau said Canada was working hard on a solution and that it was “theoretically” possible for the Canadian authorities to take back the containers.
During a visit to the area hit by Monday’s earthquake north of Manila, Duterte said he did not fear making Canadian enemies.
“I want a boat prepared. I’ll give a warning to Canada maybe next week that they better pull that thing out, or I will set sail for Canada and dump their garbage back there,” the outspoken head of state said.
“Let’s fight Canada. I will declare war against them.”
The Philippines says the containers, which arrived at the Manila International Container Port (pictured), were falsely labelled as containing plastic meant for recycling but were filled with household waste.
They contained plastic bottles and bags, household waste and soiled adult nappies, the Philippines said.
Last year Canada and the Philippines formed a working group to address the issue, but nothing has been resolved after six months.
In 2016, a Philippines court ordered the waste to be shipped back to Canada at the importer’s expense.
Other issues have strained bilateral ties.
Trudeau has been among the most vocal critics of Duterte’s thousands of drugs killings.
Human rights groups say more than 15,000 alleged drug users and street dealers have been executed, which may amount to crimes against humanity.
Duterte cancelled the Philippine military’s US$235-million contract to buy 16 helicopters from a Canadian manufacturer last year after Ottawa put the deal under review because of the Philippines’ human rights record.
A spokeswoman for Canada’s environment minister, Catherine McKenna, said work was ongoing “to ensure the material is processed in an environmentally responsible way”.
“Canada is strongly committed to collaborating with the Philippines government to resolve this issue and is aware of the court decision ordering the importer to ship the material back to Canada,” she said.
A change to regulations in 2016 was designed to prevent further shipments.
Manila International Container Port has been clogged with Canadian waste since 2013. Picture credit: Wikimedia