China on Friday challenged 2 Philippine fighter planes, one of which was carrying Defense Secretary Delfin Lorenzana en route to Pag-asa Island in the West Philippine Sea.
The Philippine planes were told to stay away from the area where the Chinese-controlled Subi reef is also located.
As the military transport plane bearing Lorenzana and local officials of Palawan island, the largest land mass close to the Spratlys, prepared to land, the minister said the pilots received a warning from Chinese forces on Subi.
He said the pilots were warned the aircraft was illegally entering Chinese territory, a routine for all Philippine aircraft landing on the Thitu airstrip since China reclaimed Subi. He said his pilots disregarded the warning.
"That's their protocol. That's procedural. We also reply that we are flying over Philippine territory," he said.
The defense chief flew to Pag-asa Island to inspect its facilities, some of which are in dire need of repair. He added that the Duterte administration is also asserting its claim over the area.
"This is just a normal visit within our territory, which we believe and we know is (our) territory," the minister told reporters who accompanied him on the brief trip.
In recent years Beijing has been building up disputed reefs into artificial islands, including on Subi Reef about 26 kilometers (14 nautical miles) from Pag-asa island, which can house military facilities.
Lorenzana said construction would start "within the next few weeks" for a quay on Pag-asa Island where construction materials will be landed for repairs on an existing airstrip on the largest of nine Philippine-garrisoned outcrops in the Spratly archipelago.
Brunei, Malaysia, Taiwan, and Vietnam also claim the Spratlys, either wholly or in part.
Lorenzana visited Pag-asa island more than a week after President Rodrigo Duterte pulled back from an announcement to visit the island on June 12 and raise the Philippine flag there.
Duterte said later he had called off the trip "because we value our friendship" with Beijing.
Reversing the course set by predecessor Benigno Aquino, Duterte has sought to improve his nation's relations with Beijing by adopting a non-confrontational approach over their competing claims in the strategically vital waters believed to sit atop huge oil and gas reserves.
Lorenzana however said Duterte was not backing down from his orders for the military to reinforce its installations in the Spratlys, and has allotted 1.6 billion pesos ($32.16 million) for these.
He said both China and Vietnam have long been fortifying their own garrisons on nearby outcrops.
"We all know that China is the most powerful country in our neighborhood, they are economically powerful, also militarily," Lorenzana said.
"We are trying manage the issue and talk to them... settle this dispute in the South China Sea."
As Lorenzana flew to Pag-asa island, the Philippine coast guard announced a group of Filipino fishermen have accused China's coast guard of shooting at their vessel in another section of the Spratlys.
Philippine officials said they were investigating the reported attack on the Princess Johann boat, which the crew said occurred near the Chinese side of the Union Banks atoll on March 27.
There were no casualties during the incident, authorities added.
"(Princess Johann) was reportedly fired upon seven times by a Chinese speedboat with seven Chinese coast guards on board," a Philippine Coast Guard statement said.
Chinese foreign ministry spokesman Lu Kang told reporters at a regular briefing that Beijing had "no information" on the matter.
If confirmed, the incident would be the first hostile episode in nearly a year involving the two countries, which have seen warming relations since Duterte came to power.
© Agence France-Presse
-- With reports from Chiara Zambrano, ABS-CBN News