MANILA (Reuters) - The Philippines will upgrade existing facilities on its inhabited islands and reefs in the South China Sea and not occupy new territories, adhering to a 2002 informal code in the disputed waters, defense and military officials said on Friday.

FILE PHOTO: A Filipino soldier patrols at the shore of Pagasa island (Thitu Island) in the Spratly group of islands in the South China Sea, west of Palawan, Philippines, May 11, 2015. REUTERS/Ritchie B. Tongo/Pool/File Photo/File Photo

A statement from Philippine President Rodrigo Duterte’s office on Thursday said he had ordered troops to occupy uninhabited islands and shoals that the Philippines claims in the disputed waterway, asserting Philippine sovereignty in an apparent change of tack likely to anger China.

The firebrand leader, who on the campaign trail joked that he would jet ski to a Chinese man-made island in the South China Sea to reinforce Manila’s claim, also said he may visit a Philippine-controlled island to raise the national flag.

But defense and military officials have subsequently clarified the president’s comments.

“The president’s order was very crystal clear. Occupy only the existing areas that we claim,” a navy commander, privy to development plans in the South China Sea, told Reuters on Friday.

“The Philippines is not allowed to do that, occupy new territories in the Spratly, based on the 2002 agreement,” said the navy official.

China’s Foreign Ministry on Friday expressed concern at Duterte’s reported remarks and said it hoped the Philippines could continue to properly manage maritime disputes with China.

China claims almost the entire South China Sea, where about $5 trillion worth of sea-borne goods pass every year. Brunei, Malaysia, the Philippines, Vietnam and Taiwan also have claims.

The president’s comments were made after he was briefed by defense and military brass about South China Sea developments in Palawan, according to his communications office. “What he really meant was the already-occupied areas,” military spokesman Brigadier-General Restituto Padilla told reporters on Thursday.

Defense Minister Delfin Lorenzana said there were plans to only repair and upgrade facilities in the Spratly.

“The president wants facilities built such as barracks for the men, water and sewage disposal systems, power generators, light houses, and shelters for fishermen,” Lorenzana said.

Another general, who also declined to be named, said there were development plans in the South China Sea in 2012, which included building a secured port on Thitu island, helicopter pads in three smaller islands, where troops are deployed.

But the plan, which also called for an increase in troop deployment in the occupied islands, was stopped after the Philippines in 2013 filed an arbitration case against China in The Hague.

The Philippines occupies nine “features”, or islands and reefs, in the South China Sea, including a World War II-vintage transport ship which ran aground on Second Thomas Shoal in the late 1990s.

The U.S. State Department declined comment on Duterte’s remarks, but has in the past urged rival South China Sea claimants to lower tensions and resolve differences in accordance with international law.