"The Philippines as an independent sovereign nation must not be treated as trash by other foreign nation," Presidential Spokesman Salvador Panelo told a media briefing.
Canada says the waste, exported to the Philippines between 2013 and 2014, was a commercial transaction not backed by the Canadian government, Presstv Reported.
Canada has since offered to take the rubbish back and the two countries are in the process of arranging the transfer.
But Canada missed a May 15 deadline set by Manila to take back the shipment, prompting the Philippines to withdraw top diplomats from Canada last week.
"Obviously, Canada is not taking this issue nor our country seriously. The Filipino people are gravely insulted about Canada treating this country as a dump site," Panelo said.
The Canadian embassy in Manila did not immediately respond to a request for comment.
The Philippines has made several diplomatic protests to Canada since a 2016 court ruling that the garbage be returned.
The consignments were labelled as containing plastics to be recycled in the Philippines but were filled with a variety of rubbish including diapers, newspapers and water bottles.
The issue is not the only one to strain ties between the two countries.
Last year, Duterte ordered the military to cancel a $233 million deal to buy 16 helicopters from Canada, after Ottawa expressed concern they could be used to fight rebels.