According to Canada's Trade Minister Francois-Philippe Champagne, the said deal struck in 2012 agreed that the helicopters would be used for search-and-rescue missions.
Earlier, Presidential Spokesman Harry Roque had said the helicopters will be used for humanitarian operations, although he kept silent on other uses for the new military hardware. "Somehow we will look for another supplier".
"When we saw that declaration... we immediately launched a review with the relevant authorities". Human rights groups have reported much higher death tolls and accused law enforcers of carrying out extrajudicial killings and of setting up crime scenes to make the victims appear to have fought back.
On Tuesday, the Philippines through Department of National Defense (DND) Secretary Delfin Lorenzana formally signed with Canadian Commercial Corporation, to purchase 16 helicopters.More news: Justin Timberlake stuns pushy 'Selfie Kid,' 13, again with Ellen's help
Mr Trudeau told journalists that he spoke with the Mr Duterte about concerns related to extrajudicial killings linked to the president's war on drugs.
The military stressed they were "utility helicopters, not attack helicopters".
Filipino officials have said the country would buy the aircraft from another source if Canada did not follow through on the deal.
In 2016, the Liberal government was criticised for deciding to honour a contract to sell light armored vehicles to Saudi Arabia, despite human rights concerns. They would be used in disaster relief efforts.More news: NVIDIA Corporation Profit Advances In Q4
The Bell H-13 Sioux, a variant of the Bell 47, was the first helicopter to enter into service with the Philippine Air Force in 1955, Bell said.
"They will be used to transport personnel, supplies, humanitarian missions, ferrying of wounded, injured soldiers and other forms of humanitarian assistance and disaster response", Roque said.
NDP foreign affairs critic Helene Laverdiere has added her voice to the chorus of concern, writing on Twitter: "How can Trudeau justify this deal with the Philippines when Duterte's government has plunged the country into a bad human rights crisis?"
Duterte, who has overseen a crackdown that has left almost 4,000 drug suspects dead at the hands of the police, later described Trudeau's comments as "a personal and official insult", adding he would only answer to his Filipino electorate. "People just don't understand", said Duterte.More news: North Korea's Kim Invites S. Korean President for Summit: S. Korea
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