The episode did not have the life-or-death drama of the April 2001 midair collision between a Chinese fighter jet and a Navy surveillance plane that forced the Americans to make an emergency landing on Chinese territory. Acknowledging the odd nature of Chinese sailors seizing the drone close to its American mother ship, one official here likened it to watching a thief steal a wallet in broad daylight.
American officials said they were still trying to determine whether the seizure was a low-level action taken by Chinese sailors who spotted the drone — which the Pentagon said was conducting scientific research — or a strategic-level action ordered by more senior Chinese leaders to challenge the American presence in those waters.
“We call upon China to return” the underwater vehicle “immediately,” Peter Cook, the Pentagon press secretary, said in a statement Friday, “and to comply with all of its obligations under international law.”
The incident complicates already testy relations between China and the United States, ties that have been further frayed by President-elect Donald J. Trump’s phone call with the president of Taiwan. Mr. Trump angered Chinese officials by holding a phone conversation with President Tsai Ing-wen of Taiwan, an island that Beijing deems a breakaway province of China. It had been nearly four decades since a United States president or president-elect had such direct contact with a Taiwanese leader.
In an interview broadcast on Sunday, Mr. Trump also criticized China over its trade imbalance with the United States, its military activities in the South China Sea and its links to North Korea. Aides to the president-elect have defended Mr. Trump’s words and actions as important to bringing a fresh eye to a number of foreign policy issues.
Pentagon officials said on Friday that they were trying to determine if the seizure of the underwater drone had anything to do with Mr. Trump’s comments.
At the White House on Friday, President Obama was asked about the issue during a news conference, and he made clear that he viewed the question of Taiwan as especially sensitive. While the president refrained from directly criticizing Mr. Trump, he warned his successor to carefully consider his actions and any new policy, lest he ignite what could be a significant response from Beijing.
“I think all of our foreign policy should be subject to fresh eyes,” Mr. Obama said. But he added: “For China, the issue of Taiwan is as important as anything on their docket. The idea of a One China is at the heart of their conception of a nation.”
“And so if you are going to upend this understanding, you have to have thought through what the consequences are, because the Chinese will not treat that the way they’ll treat other issues,” he said, adding that the Chinese would not even treat it the way they treated issues around the South China Sea, “where we’ve had a lot of tensions.”
China experts said on Friday that it was unclear whether the seizure of the American drone was linked to anger in Beijing over Mr. Trump, or a continuation of years of tensions over competing claims in the South China Sea.
The Bowditch episode came after China signaled on Thursday that it had installed weapons on disputed islands in the South China Sea that it would use to repel threats. In describing the new weapons deployment, a Defense Ministry statement suggested that China was further watering down a pledge made by its president, Xi Jinping, to not militarize the islands.
That indicated that such installations were part of China’s plan to deepen its territorial claim over the islands, which has created tensions with its neighbors over their rival claims and with Washington over freedom of navigation in the South China Sea, one of the world’s busiest commercial waterways. The United States Navy routinely sends warships to sail the South China Sea as part of ongoing American policy meant to demonstrate that all countries have the freedom of navigation in disputed waters.
M. Taylor Fravel, an associate professor of political science at M.I.T. who studies China’s territorial disputes and has written on the South China Sea, called the seizure of the drone “a big deal, as it represents the deliberate theft of U.S. government property and a clear violation” of maritime law.
“By stealing a drone versus threatening the safety of the ship, China may be trying to find a way to signal its opposition to U.S. activities without creating a larger incident,” Mr. Fravel said.
“Nevertheless, it will be viewed by the U.S. as a clear challenge.”
The Bowditch, an oceanographic ship, was operating in international waters and carrying out scientific research, said Capt. Jeff Davis, a Pentagon spokesman. The drone was part of an unclassified program to collect oceanographic data, including salinity in the sea, clarity of water and ocean temperature, factors that can help the military in its collection of sonar data.
The Chinese Navy ship, which had been shadowing the American ship, approached within 500 yards of the Bowditch before seizing the drone, which American officials say was around 50 nautical miles northwest of Subic Bay, the Philippines.
Whatever the case, the Pentagon said that China had no right to seize the drone. “This is not the sort of conduct we expect from professional navies,” Captain Davis said.
Michael Swaine, a senior fellow at the Carnegie Endowment for International Peace, called the theft “low-level provocation.”
“This doesn’t involve lives,” Mr. Swaine said. “It involves the Chinese grabbing something that belongs to the United States. The normal thing to do in these cases is, you issue a démarche and demand it be returned ASAP.”
Senator John McCain, Republican of Arizona, criticized the Obama administration for what he called a failure to provide a “strong and determined U.S. response” to Chinese actions in the South China Sea. “Freedom of the seas and the principles of the rules-based order are not self-enforcing,” he said. “American leadership is required for their defense. But that leadership has been sorely lacking.”
There was no immediate comment from Mr. Trump or his transition team.