MANILA (Reuters) - The Philippines is withdrawing top diplomats from Canada after Ottawa missed a deadline to take back 69 shipping containers full of trash, the latest move in a long-running row stoked by threats from Manila's outspoken president.

Last month, President Rodrigo Duterte threatened Canada with war and said he would personally escort the waste containers by sea back to Canada.

"We shall maintain a diminished diplomatic presence in Canada until its garbage is ship-bound there," Philippine Foreign Secretary Teodoro Locsin said on Twitter on Thursday after the May 15 deadline expired.

In a statement, Canada's foreign ministry said it was "disappointed", but would continue to engage to resolve the issue.

"Canada has repeatedly conveyed to the Philippines government its commitment to promptly ship and dispose of the Canadian waste in the Philippines," the statement said. "We remain committed to finalizing these arrangements for the return of the waste to Canada."

Locsin also took issue with Philippine diplomats for not doing enough to ensure Canada took back the trash, accusing them of acting in defiance of their president to preserve friendly relations.

The volatile 74-year-old Duterte, known for his grandstanding and often hollow threats toward Western powers, has also said he would dump the trash in front of Canada's embassy in Manila.

Canada says the waste, exported to Manila between 2013 and 2014, was a commercial transaction not backed by its government. It has since offered to take it back and the two countries were in the process of arranging the transfer.

The Philippines has made several diplomatic protests to Canada after a 2016 court ruling that the garbage be returned.

The consignments were labeled as containing plastics to be recycled in the Philippines, but were filled with diapers, newspapers and water bottles instead.

(Reporting by Neil Jerome Morales; Additional reporting by Steve Scherer in OTTAWA; Editing by Martin Petty, Clarence Fernandez and Susan Thomas)