BEIJING—A U.S. think-tank report that China has installed antiaircraft weapons and other arms on all seven islands it has built in the South China Sea is raising the stakes in a regional dispute as U.S. President-elect Donald Trump signals he is ready to confront Beijing on territorial issues.

The Asia Maritime Transparency Initiative said Wednesday that satellite imagery showed China had installed the weapons in recent months, despite President Xi Jinping’s pledge not to militarize the islands in the Spratly archipelago, where Beijing’s territorial claims overlap with those of several other governments.

China’s Defense Ministry reiterated in a statement on its website Thursday that any reef construction was mainly for civil use, though it appeared to also send a message to the U.S. “As to the necessary military facilities, they are mainly for defense and self-defense, which is appropriate and legal. For example, if someone is showing off their strength on your doorstep, can’t you even prepare a slingshot?” the statement said.

China’s island-building over the past three years has raised fears in the U.S. and among its Asian allies and partners that Beijing plans to use its expanding military power to enforce its territorial claims and to take control of a shipping route that carries more than $5 trillion of world trade annually.

In Washington, Sen. John McCain (R., Ariz.), chairman of the Senate Armed Services Committee, blasted the Chinese and demanded the U.S. take action against the weaponry.

“It appears China is intent on transforming these features into operational bases that will allow its military to project power and assert control of one of the most vital international waterways,” he said. “This is unacceptable.”

The Chinese have been emplacing small weapons on the reclaimed islands for months, adding weapons to three more individual islands since August, a senior U.S. military official said. But the systems the Chinese have installed have extremely limited ranges, of between one and two miles, the official said. These are considered low-level “point defenses,” meaning they are capable mainly of defending the immediate area around the islands where they are located.

Most U.S. naval vessels transiting the area, even those conducting so-called freedom of navigation operations, don’t sail within that distance of the islands, military officials have said.

Although not seen as a significant military threat, the weapons are considered modular, meaning the current weapon mounts could be used to support larger, more serious surface-to-air missiles, the military official said.

“It’s certainly part of what we have seen as the continuum of the progress of what the Chinese are doing there,” the official said. “This is a classic case of the frog slowly boiling.”

Adm. Harry Harris, commander of the U.S. Pacific Command, said in a speech at an Australian think tank on Wednesday that the U.S. “will not allow the shared domains to be closed down unilaterally no matter how many bases are built on artificial features in the South China Sea.”

He added, “We will cooperate where we can and be ready to confront where we must.”

The U.S. has sent military planes and ships through the area, sometimes close to Beijing’s artificial islands, to demonstrate its right to freedom of navigation through what it sees as international waters. Following Wednesday’s report, the State Department reiterated its call for Beijing to refrain from further development and militarization in the disputed waters.

Mr. Trump has indicated he will take a harder line than his predecessor toward China, suggesting in the past two weeks that he would review U.S. commitments on the highly sensitive issue of Taiwan and accusing Beijing of building a “massive military complex” in the South China Sea.

Those comments have revived tensions in the region, which had appeared to ease over the past months, in particular as Philippine President Rodrigo Duterte set aside Manila’s South China Sea dispute with Beijing in favor of expanding economic links.

“If the [AMTI] report is true, then it is a cause for serious concern because it tends to raise tension and undermine peace and stability in the region,” Philippine Department of Foreign Affairs spokesman Charles Jose said.

Australian Foreign Minister Julie Bishop echoed the sentiment. “The building of artificial islands and the possible militarization is creating an environment of tension and mistrust between claimants and other regional states,” she said. Canberra signed a deal on Wednesday with Washington to base U.S. F-22 Raptor stealth jet fighters in Australia’s north from next year, a sign of the U.S. military commitment to the region.

China’s weapons deployment predates Mr. Trump’s recent remarks and is in line with Beijing’s long-term strategy to steadily upgrade military facilities on the islands, which it says are mainly for purposes such as weather monitoring and search and rescue.

“I want to stress that deployment of necessary defense facilities by China on its own territory has nothing to do with militarization,” said Foreign Ministry spokesman Geng Shuang on Thursday.

But analysts say the new weaponry will significantly enhance China’s capability to control the surrounding waters and to enforce a potential air-defense identification zone in the area like the one Beijing declared in 2013 over the East China Sea, where it has a territorial dispute with Japan. China has said it reserves the right to declare such a zone—within which it reserves the right to identify, communicate with and intercept approaching foreign aircraft—in the South China Sea as well.

The deployments are unlikely to disrupt Beijing’s outreach to other claimants, but could compound efforts by some to upgrade defense ties with the U.S. and their own armed forces; Vietnam, especially, has been expanding the South China Sea islands it controls—although on a much smaller scale.

“We mustn’t interpret this as being specifically directed at President-elect Trump,” said Ian Storey, an expert on maritime security at the Institute of Southeast Asian Studies in Singapore. “Nevertheless, it will fuel the debate in Washington over how the U.S. should respond to Beijing’s actions in the South China Sea.”

Mr. Storey said the U.S. might send military ships or planes near China’s man-made islands to demonstrate its right to freedom of navigation once more before President Barack Obama leaves office, operations that have become largely symbolic. “Beijing will be more concerned about what happens after Trump is inaugurated in January, he added.

AMTI, run by the Center for Strategic and International Studies in Washington, said that since June and July it had tracked construction of hexagonal structures on three artificial islands—Fiery Cross, Mischief Reef and Subi Reef—where China has built airstrips large enough to accommodate military aircraft.

Those structures are nearly identical to defensive fortifications built earlier at four smaller artificial islands, which appear to include antiaircraft guns and probably close-in weapons systems, or CIWS, designed to track and shoot down cruise missiles, AMTI said.

AMTI said the weapons it identified could be used to back up a defensive umbrella provided by a future deployment to the islands of mobile surface-to-air missile systems.