China's militarisation of the South China Sea is "very troubling" and neither peaceful nor friendly, the Philippines' defence secretary said on Tuesday.

President Rodrigo Duterte has sought to improve his nation's relations with China by adopting a non-confrontational approach over their competing claims in the strategically vital waters.

But, even as other senior government officials sought to downplay China's building of defence installations on artificial islands it has built in the sea, Defence Secretary Delfin Lorenzana issued a strongly worded statement.

"Notwithstanding the warming of relations between our countries, the Philippine government would be remiss in its duty to protect its national interest if it does not protest, question and seek clarification from China on the presence of weapons in the Spratlys," Lorenzana said in a statement.

"The actions of China in militarising those disputed features are very troubling. They do not square with the Chinese government's rhetoric that its purpose is peaceful and friendly."

Lorenzana released the statement hours before President Duterte was scheduled to meet with Chinese Vice Foreign Minister Liu Zhenmin.

Foreign Secretary Perfecto Yasay had earlier said the Philippines had quietly sent a diplomatic note to Beijing last month over the reports of Chinese missile installations in the Spratlys, a South China Sea chain.

But he said this was done in a low-key way so as not to anger China.

The US-based Center for Strategic and International Studies released photos in December that it said showed China appeared to have built large anti-aircraft guns and other weapons systems at each of its seven outposts in the Spratlys.

China said after the images were released that the deployment of weapons in the South China Sea had "nothing to do with militarisation", and called the construction of defensive facilities "normal".

China claims most of the South China Sea, even waters and outcrops approaching the coasts of the Philippines and other Southeast Asian neighbours.

An international tribunal last year ruled that China's claims over the sea over the sea, through which more than five trillion dollars in global shipping trade passes, had no legal basis.

Even though China is a signatory to the UN Convention on the Law of the Sea, on which the case was based, it rejected the ruling.

The legal suit was filed by the administration of Duterte's predecessor, Benigno Aquino.

But when the Philippines won the case, Duterte was already president and pursuing closer ties with China. He vowed not to "taunt or flaunt" the ruling.