Manila has ordered Beijing to recall 183 boats at the boomerang-shaped reef around 320 kilometres (175 nautical miles) west of Palawan Island, describing their presence as an incursion of its sovereign territory.
Around 220 boats were detected by the Philippine coast guard on March 7 but only made public last weekend. A military aerial patrol over the reef on Monday found 183 were still there.
China says the fishing boats are sheltering from poor weather near the reef, which it claims is part of the contested Spratly Islands.
A spokesman for the Armed Forces of the Philippines said the additional navy ships would carry out “sovereignty patrols” in the waterway.
He did not say if the ships would go near the reef or what type of vessels would be used.
Beijing often invokes the so-called nine-dash line to justify its apparent historic rights over most of the South China Sea, parts of which are also claimed by Taiwan, Malaysia, the Philippines and Brunei.
Duterte met with the Chinese ambassador to the Philippines this week and expressed concern over the presence of the vessels, presidential spokesman Harry Roque said Thursday.
But Roque said there was “no real controversy since they (the Chinese) are not insisting to stay there permanently.”