The containers full of rubbish were loaded onto ships overnight and sent off on a 20-day trip to Vancouver, leading to cheers of support from environmental activists who protested wealthier nations sending their rubbish to Asia.
The decision comes after the Philippines' president, Rodrigo Duterte, threatened to forcibly send the waste back after it originally arrived in 2013 and 2014.
Some of the rubbish had already been dumped in a landfill, however, leaving household waste like diapers and electronics wasting away in Philippine ports.
“I think the message that we’re sending to the world is that we will not be a pushover and, moreover, that the president is really somebody to reckon with,” said Wilma Eisma, the administrator in the Subic Bay port.
Mr Duterte was not president when the contentious issue began six years ago, but had promised to send the rubbish back in light of widespread international criticism of the way he has run his government.
Justin Trudeau, the Canadian prime minister, has also denounced Mr Duterte’s deadly crackdown on illegal drug use, which has killed thousands of people.
Mr Trudeau had reportedly been working to resolve the issue with the Philippine government, but had cited legal issues as a barrier to returning the garbage to the country.
Mr Trudeau has said the rubbish was originally shipped to Manila in a private commercial transaction.
Additioanl reporting by Associated Press
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