The 69 containers of trash will be loaded onto cargo ship MV Bavaria in a northern port, Filipino Administrator Wilma Eisma of Subic Bay said.
The Liberals have been negotiating with the Philippines about the garbage for the last 3½ years, finally agreeing to bring the remaining waste back and pay for the shipments in April, after Duterte threatened to "declare war" on Canada.
"The troubling question is why for six years did Canada refuse to comply with what were clearly its legal obligations to bring back the waste", she said, referring to Canada's obligations under an worldwide treaty called the Basel Convention.
Philippine Foreign Secretary Teddy Locsin posted video and photos to his Twitter account showing the containers being loaded throughout the afternoon and into the wee hours of the morning in Subic, a major global port northwest of Manila. The former Conservative government spent more than two years trying to convince the Philippines to dispose of the trash there, and in July 2015, the contents of 26 of the containers were dumped into a local landfill.
The Philippines government recalled its ambassador and consuls in Canada earlier this month over Ottawa's failure to comply with a May 15 deadline to take back the waste. She added that all of the containers have been fumigated and were loaded on board Thursday. The move could possibly end a six-year dispute between the two countries.More news: Moto Z4 price and specifications confirmed courtesy of Amazon listing
The countries had sought to resolve the problem for years, with Canadian Prime Minister Justin Trudeau saying in 2017 that legal issues preventing the return of the garbage had been resolved.
A Canadian official confirmed the ship is hired under a $1.14-million contract Canada signed with the Canadian arm of French shipping giant Bollore Logistics to bring the garbage back to Canada.
The return, however, was delayed by other issues despite Canadian assurances of its willingness to take back the rubbish that Mr Trudeau said was shipped to Manila in a private commercial transaction.
"The president's stance is as principled as it is uncompromising: The Philippines as an independent sovereign nation must not be treated as trash by other foreign nations".
There were 69 containers carrying wastes which were shipped to the country from Canada from 2013 to 2014.More news: NASA has selected the first three companies bringing payloads to the moon
A Malaysian environmental official on Tuesday vowed to send back 3,300 tons of non-recyclable plastic waste back to Western countries, including the U.S.
Speaking in Tokyo on Thursday, Mahathir said it was "grossly unfair" and should stop.
Last week, Malaysia announced it would return thousands of tonnes of contaminated recycling to their countries of origin - including Canada.
"This ordeal has taught us of the urgency of correcting outmoded regulations allowing waste imports into the country under the guise of recycling", said Aileen Lucero, the national co-ordinator of EcoWaste Coalition, an environmental organization in the Philippines, in a joint release that included RightOnCanada.
They cited the discovery of other waste shipments to the Philippines from South Korea in 2018 and more recently from Australia and Hong Kong.More news: Fans and drivers remember F1 legend Niki Lauda at funeral