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Canada says it will take back tonnes of waste shipped to the Philippines, causing a diplomatic stink.

The federal environment minister's announcement came shortly after Philippines President Rodrigo Duterte ordered the rubbish sent back.

The Philippines has filed several diplomatic protests over the refuse that was shipped between 2013-14.

A private company contracted by Canada is expected to begin preparation for shipment in the coming days.

Environment Minister Catherine McKenna said on Wednesday that Canada will cover the full costs of the preparation, transfer, shipment, and disposal of the waste and complete the transfer by the end of June.

Last week, Manila recalled its ambassador to Ottawa after Canada missed a 15 May deadline to retrieve the rubbish - part of a growing row over the longstanding irritant.

"As a result of this offending delay, the president has instructed the appropriate office to look for a private shipping company which will bring back Canada's trash to the latter's jurisdiction," Duterte spokesman Salvador Panelo told reporters on Wednesday.

"If Canada will not accept the trash, we will leave the same within the territorial waters or 12 nautical miles out to sea from the baseline of any of their country's shores."

Mr Duterte, who is known for his outspoken style, had threatened last month to ship the waste back if the issue was not resolved.

The row relates to containers shipped to Manila by a private Canadian-based company and its Philippines-based consignees.

Manila says the containers, which arrived at Manila International Container Port, were falsely labelled as containing plastics meant for recycling and were in fact filled with tonnes of household waste.

Another inspection of the remaining containers in 2015 found they contained non-hazardous municipal waste, including household and street rubbish.

The government says the containers have caused port congestion and are a hazard to public health.

Some remain in storage at the Manila port while others have been disposed of in a large landfill site.

In 2016, a court in the Philippines ordered the waste to be shipped back to Canada at the expense of the importer.

That same year, Canada amended its own regulations around hazardous waste shipments to prevent a repeat of this situation.