Following a joint Air Force and Navy drill in the contested waterway, China says it will continue to defend its national sovereignty.
China's relationship with South China Sea neighbors is often contentious.
Defense Secretary Jim Mattis said the U.S. was encouraged by China's efforts to restrain North Korea but challenged China's placing of weapons and other military assets on man-made islands.
The move is likely to anger China after a detente between Trump and President Xi Jinping following a meeting in Mar-a-Lago.
The president's unpredictability is worrying America's friends abroad, but there are signs that his hardline, "America First" isolationism is softening.
Fiery Cross Reef is administered by China but also claimed by the Philippines, Vietnam and Taiwan.
Malaysia, the Philippines, Vietnam, Japan, and China all claim parts of the South China Sea.
Manila is looking to ease tensions with Asia's top economic power.
Though the U.S. has not run any freedom of navigation patrols since Trump became president, the policy of testing China had not changed, said the Pacific Fleet Commander.
Members of the Association of South East Asian Nations (ASEAN) will adopt a softer than usual tone about South China Sea disputes at a leaders' summit on Saturday in Manila.
The Philippines president has abandoned his plan to plant a flag on the Spratlys.
The United States has said in the past that rotational deployments of Chinese fighter jets to Woody Island were part of a disturbing trend of militarization.
The Chinese defense ministry said that, despite an upcoming massive arms deal from President Donald Trump, there was 'no way out' for Taiwan.
The Asia Maritime Transparency Initiative (AMTI) said the work on Fiery Cross, Subi and Mischief Reefs in the Spratly Islands included naval, air, radar and defensive facilities.
Diplomats briefed on latest Western intelligence assessments say Beijing is pursuing efforts to dominate its maritime 'backyard.'
The move will be Tokyo's biggest show of naval force in the region since World War II.