The remarks came after an aerial inspection of Scarborough Shoal on Thursday confirmed a 300 metre (328-yard) barrier that ignited the latest diplomatic row between Beijing and Manila had been taken away.
AFP journalists were on board a Bureau of Fisheries and Aquatic Resources' plane as it flew over the Chinese-controlled reef and saw access to its shallow waters unblocked.
The floating barrier was found across the entrance to the shoal last week during a routine Philippine government resupply mission to Filipino fishermen.
In a special operation ordered by President Ferdinand Marcos, Philippine Coast Guard personnel cut a rope tethering the barrier to an anchor, allowing it to drift.
"In the next coming months, if ever that barrier will once again be in place, the Philippine Coast Guard will do whatever it takes for us to remove the barrier," coast guard spokesman for the West Philippine Sea Jay Tarriela told reporters, as he sat next to the anchor seized during the mission.
In his first public remarks on the incident, Marcos said Friday that his government was "not looking for trouble".
But he insisted it would "continue to defend the Philippines, the maritime territory of the Philippines, the rights of our fishermen to ply their trade in the areas where they have been fishing for hundreds of years."
Earlier this week, China warned the Philippines not to "stir up trouble" over the incident that has ignited a war of words between the countries.
China Coast Guard said Wednesday it had deployed the line of buoys after the Philippine vessel's "intrusion into the lagoon" and removed them on Saturday.
"The on-site operation was professional and standard, legitimate and rational," spokesman Gan Yu said in a statement.
- 'Bold step' -
China, which claims almost the entire South China Sea, seized Scarborough Shoal from the Philippines in 2012.
Since then, Beijing has deployed patrol boats that Manila says harass Philippine vessels and prevent Filipino fishermen from reaching the lagoon where fish are more plentiful.
During Thursday's aerial surveillance, officials identified three Chinese coast guard ships, including two inside the reef, which issued six radio challenges to the aircraft.
A fourth vessel was described as a "militia" boat.
A small number of Filipino fishing boats was also spotted outside the turquoise waters of the shoal.
A senior US defence department official on Thursday praised the Philippines' actions to remove the barrier as a "bold step" and said the United States stood by its security commitments to the country.
"The department has been incredibly clear that when it comes to our treaty commitments to the Philippines, we believe an armed attack against Philippine Armed Forces, public vessels, aircraft, apply to the South China Sea. That includes the Philippine Coast Guard," Deputy Assistant Secretary of Defense for South and Southeast Asia Lindsey Ford told a congressional hearing.
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