The Philippines will lodge a diplomatic protest with China after Manila questioned if Beijing had reneged on a pledge not to militarise a disputed South China Sea reef.

Beijing claims nearly all of the sea and has been turning reefs in the Spratly and Paracel chains into islands, installing military facilities and equipment on them.

Defence Secretary Delfin Lorenzana Tuesday said Manila was investigating reports of recent Chinese activity on Fiery Cross Reef, an outcrop that Beijing turned into an artificial island and which now appears to house a military base.

Lorenzana spoke out despite recent moves by President Rodrigo Duterte to ease tensions with China.

"According to them they are not militarising (the reefs) and it was for peaceful purposes only like tourism," Lorenzana said.

"But if it is true and we can prove that they have been putting soldiers and any weapons, defensive (or) otherwise, that would be a violation of what they said".

Lorenzana said he had also received reports Philippine fishermen had been "harassed" by Chinese coastguards.

Asked about the Philippine complaints, Chinese foreign ministry spokesman Lu Kang said China "is conducting peaceful construction in our own territory", and that Beijing "has the need to build necessary territorial defence equipment".

He added: "It's not targeted at any country. I need to point out that China and the Philippines are friendly, neighbours."

Last month, a US think tank released new satellite images showing deployment of radar and other equipment in disputed South China Sea islands.

The Asia Maritime Transparency Initiative (AMTI) said the buildup continued despite rival claims across the sea from Vietnam, the Philippines, Malaysia, Brunei and Taiwan.

Over 2017, China installed infrastructure to support air and naval bases, such as "large radar and sensor arrays", the Washington-based think tank said.

Fiery Cross Reef saw the most construction last year, with building work spanning 27 acres, or about 110,000 square metres, AMTI said its analysis of satellite images showed.

The Philippines had previously been one of the most outspoken countries in standing up to China's claim to most of the South China Sea.

This culminated in Manila's complaint to a United Nations-backed tribunal that ruled in July 2016 that China's territorial claims in the sea were without legal basis.

But since Duterte took office in mid-2016, he has decided not to use the ruling to pressure China but has instead chosen to build closer ties in return for billions of dollars in investment and aid.