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 ship is scheduled to head to Canada on Friday.
Transporting the garbage to Canada will seemingly end a daunting feud between Filipino President Rodrigo Duterte and Canadian Prime Minister Justin Trudeau.
The Great White North shipped more than 100 containers of household trash, including plastic bottles and bags, newspapers and used adult diapers to the Philippines from 2013 to 2014. Officials have said the shipments of waste were incorrectly declared by a private firm as recyclable plastic scraps.
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.
In recent months, the Philippines told Canada to take the garbage back. In April, Duterte threatened to "declare war" if the garbage was not removed, and later said he would take the garbage and dump it on Canada's beaches.
A spokesperson for the president later said that both of Duterte's comments are "figures of speech," and that the former was "an expression of outrage."
The Philippines recently recalled its ambassador and consuls in Canada over Ottawa's failure to comply with the May 15 deadline Duterte set to take back the garbage. Trudeau said that Canada had been working hard with Philippine officials to find a resolution, but didn't specify a time frame.
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.
The prime minister, Mahathir Mohamad, has also criticized the practice of wealthier countries such as the U.S., Canada and Japan sending their non-recyclable waste to poorer countries. He called it "grossly unfair" and said it needs to stop.
Fox News' Paulina Dedaj and The Associated Press contributed to this report.