WASHINGTON — Six weeks ago, the United States Pacific Command requested permission from senior American officials for a United States warship to sail within 12 nautical miles of Scarborough Shoal, a disputed reef in the South China Sea that is claimed by the Philippines and China.
The Navy had good reason to think the request would be granted. During last year’s campaign, President Trump labeled then-President Barack Obama as weak in defending international waters in the South China Sea, where Beijing has started a sharp military buildup to reclaim land, install runways and haul equipment onto reefs and shoals it claimed as its own. Secretary of State Rex W. Tillerson, during his confirmation hearing in January, called for China to be denied access to the artificial islands. And foreign policy experts and Asia watchers braced for a return to routine Navy patrols within China’s self-proclaimed territorial waters, something Mr. Obama allowed sparingly.
But instead, the Pacific Command request — and two others by the Navy in February — was turned down by top Pentagon officials before they even made it to Mr. Trump’s desk. More than 100 days into the Trump presidency, no American Navy ship has gone within 12 miles of any of the disputed islands in the South China Sea, Defense officials said.
The decision not to challenge China’s territorial claims shows a remarkable deference toward Beijing from an administration that is increasingly turning toward Chinese President Xi Jinping for help amid the escalating crisis in the Korean Peninsula. It remained unclear on Tuesday whether it was Defense Secretary Jim Mattis; Gen. Joseph F. Dunford Jr., the chairman of the Joint Chiefs of Staff; or one of their deputies who turned down the three requests. Defense officials said that the White House was not involved.
“All of the language, combined with the fact that the Republican foreign policy establishment had been critical of Obama for not carrying out enough Fonops, means there was a wide expectation that Trump would put down a marker early. And that hasn’t happened,” said Robert Daly, the director of the Kissinger Institute on China and the United States at the Wilson Center. He was referring to the Navy excursions, officially known as freedom of navigation operations.
The simmering crisis in North Korea seems to have changed the Trump administration’s earlier assumptions on how to handle China. Mr. Trump campaigned on being tough on Beijing, promising that he would label China a currency manipulator and would go after Beijing on trade.
But as North Korea accelerated its provocative behavior the past three months, attempting nine missile launches on six occasions since Mr. Trump came to power, his administration has adopted a more conciliatory air with Beijing as the president seeks help to rein in Pyongyang.
With each missile launch, Mr. Trump’s newfound affection for the Chinese leader, Mr. Xi, has increased. Last Saturday, after the most recent launch, Mr. Trump wrote on Twitter that North Korea had “disrespected the wishes of China and its highly respected president when it launched, though unsuccessfully, a missile today. Bad!”
Decisions to deny the Navy’s requests to sail within 12 nautical miles of disputed islands in the South China Sea were fairly routine during the Obama administration. In fact, that Mr. Obama came under sharp criticism from Republicans for suspending for more than two years of such excursions, out of concern for further raising tensions with Beijing.
In October 2015, the Obama administration sent a guided missile destroyer, the Lassen, within territorial waters near Subi Reef, one of several artificial islands that China has built in the disputed Spratly Islands chain. At the time, Mr. Obama’s White House played down the episode and directed Defense Department officials not to talk about it publicly, wanting to avoid escalating a conflict.
Such hesitance prompted harsh words from Mr. Trump during the presidential campaign. In an interview with The New York Times in March 2016, Mr. Trump said that Beijing had built in the South China Sea “a military fortress, the likes of which perhaps the world has not seen.
“Amazing, actually,” he said. “They do that at will, because they have no respect for our president and they have no respect for our country.”
Mr. Tillerson came to office saying that China’s island-building campaign was “akin to Russia’s taking of Crimea.” He said that the Trump administration was “going to have to send China a clear signal that, first, the island-building stops,” and “second, your access to those islands also is not going to be allowed.”
That denial of access is now on the back burner. In fact, China has continued to militarize the islands, according to Mr. Daly, of the Wilson Center, and has bomb-proofed airplane hangars that were built on the reclaimed islands as well as brought in additional equipment.
Chinese officials have maintained that such action does not constitute militarizing the islands. They say the islands are Chinese territory and Beijing therefore cannot militarize land it already owns. The United States and other countries disagree.
The Chinese have not yet begun construction on Scarborough Shoal. American officials have long viewed doing so as something of a red line, and have cautioned Chinese counterparts that any building on the shoal would be viewed as provocative.
Mr. Obama warned Mr. Xi at a March 2016 meeting in Washington not to start building an island at Scarborough Shoal. Late last year, an unusually large number of Chinese vessels were positioned close to the disputed reef, renewing American concerns.
A Defense official described the Pacific Command request last month to conduct a naval excursion within 12 nautical miles of Scarborough Shoal as a signal to the Chinese that building on the atoll remained a red line for the United States. The official, who spoke on condition of anonymity to discuss sensitive operations more frankly, added that Navy officials believed that the request to be in line with what the Trump administration wanted.
But Defense officials also said that Mr. Mattis and the Pentagon leadership want to look carefully at the strategic implications of such excursions on overall national security policy. While Mr. Mattis is far from opposed to the freedom of navigation trips, he is reviewing the American security posture around the world, Defense officials said.
Additionally, Washington’s hope that China will rein in North Korea has called into question the timing of the next freedom of navigation sail.
Andrew L. Oros, the author of the newly published “Japan’s Security Renaissance,” said that it was far more important now to address North Korea’s missile and nuclear weapons development than to pick a fight over the Navy navigation trips.
“That’s clearly the case,” Mr. Oros said. But, he said, the Trump administration still must
closely monitor China’s activities and not give ground in the disputed islands.
“ And I hope this doesn’t give the Chinese the impression that this is a tacit acknowledgment of Beijing’s outrageous claims of sovereignty over international waters,” he said.