President Rodrigo Duterte went on to assure China no "offensive weapons" would be placed there.
He said the Philippines wanted peace and friendship with China but his country needed to bolster what territory it had in the Spratly archipelago because "everybody's grabbing" islands and reefs in the disputed waterway.
The maverick former mayor set off alarm bells on Thursday, including in Beijing, when he said he had ordered troops to occupy uninhabited islets and shoals that the Philippines claims in the Spratly Islands.
Philippine president Rodrigo Duterte says no 'offensive weapons' will be placed in waters
Philippine officials later said plans were to upgrade existing facilities and not occupy new territories.
I ordered the occupation of the 10 or nine islands that are just near our shores
Philippine President Rodrigo Duterte
President Duterte said: "I'd like to address myself to the Chinese government…
"I ordered the occupation of the 10 or nine islands that are just near our shores because there's a heightening of geopolitical issues and eventually maybe a violent low-intensity war over here."
He said the Philippines would not engage in any military buildup, but indicated the United States would.
Chinese aircraft carrier fleet in training at South China Sea
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Armed police soldiers lift timbers during a drill on August 24, 2016 in Chongqing, China. As the highest temperatures reached over 40 degree Celsius at 5 districts in Chongqing, officers and soldiers of an armed police crop took outdoor training
China claims most of the South China Sea through which about $5 trillion in ship-borne trade passes annually.
Brunei, Malaysia, the Philippines, Taiwan and Vietnam also have claims.
President Duterte has turned Philippine foreign policy upside down by making overtures towards China and fiercely rebuking traditional ally the United States. Duterte wants China to be a major investor in the Philippines.
He puts the blame for current maritime tensions squarely on Washington, for not intervening to stop China building and arming artificial islands in the Philippines' exclusive economic zone.
He said: "If they fight each other, we will be hit. Everybody knows, the United States will be stockpiling their weapons there. And, they said they will not.
President Duterte said the Philippines wanted peace and friendship with China
"I do not want to get involved in a war between nations. I have extended my hand and friendship to the US government."
He seldom criticises China for its actions in the South China Sea and stressed on Monday that any future Philippine activities in the Spratlys would not be hostile.
President Duterte said: "For the information of China, we will not place there any offensive weapons, not even one gun."
China's Foreign Ministry spokeswoman Hua Chunying told a regular briefing there was "close and effective communication" between Beijing and Manila.
She said: "We hope the Philippines can move forward with China and continue to appropriately handle disputes and create a good atmosphere."