President Rodrigo Duterte says he instructed the military to assert Philippine ownership of a large ocean region off the country's northeastern coast where China's survey ships were spotted last year.

However, Duterte said on Monday he ordered the military to claim the Benham Rise area in a friendly way, repeating that his country has no option but to be diplomatic because it "cannot match the might of China".

"My order to my military, you go there and tell them straight that this is ours, but I say it in friendship," Duterte said in a news conference when asked about the issue in the Pacific Ocean.

The Philippine military spotted the Chinese survey ships suspiciously crisscrossing the Benham Rise waters from July to December last year, defence chief Delfin Lorenzana said last week.

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Lorenzana said the government is considering an increase in patrols and the building of territorial markers in the offshore region, which is believed to be rich in mineral resources and a vast coral reef ecosystem.

The Chinese ships' presence in the area was to be discussed late on Monday at a meeting between National Security Council executive members and Duterte.

The Department of Foreign Affairs said it asked China through its embassy on Friday to clarify what the survey ships were doing in Benham Rise.

In 2012, the UN Commission on the Limits of the Continental Shelf declared Benham Rise to be part of the Philippine continental shelf, where the country has exclusive rights to fish and exploit resources, including undersea deposits of oil and gas.

'Innocent passage'

The Chinese foreign ministry has said its ships have a right to "innocent passage" through the area under international law.

Beijing and Manila have a separate long-running territorial feud in the South China Sea west of the Philippines, but tensions have eased considerably since Duterte took office in June and began reaching out to China.

He has placed the dispute on the backburner while seeking Chinese trade and economic aid, downplaying the issue during his visit to Beijing last year.

Duterte has also shelved plans made under his predecessor for joint Philippine patrols with the US Navy in disputed waters to avoid offending China.

A US Navy aircraft carrier, the USS Carl Vinson, has been sailing on a mission to ensure freedom of navigation in the South China Sea, claimed virtually in its entirety by China.

"America wants to pick a fight there," said Duterte, who has openly criticised US security policies. "Why would I get into a trouble in that area?"