The top U.S. commander in the Asia-Pacific, Admiral Harry Harris, told the U.S. Congress that the Terminal High Altitude Area Defense (THAAD) system would be operational "in coming days."
The earlier-than-expected steps to deploy system were denounced both by China, and the frontrunner in South Korea's presidential election on May 9.
South Korea's defence ministry said elements of THAAD were moved to the deployment site, on what had been a golf course, about 250 km (155 miles) south of the capital, Seoul.
It said South Korea and the United States had been working to reached "early operational capability" and the battery was expected to be operational by the end of the year.
Harris, testifying before the U.S. House Armed Services Committee, said THAAD "will be operational in the coming days."
The United States and South Korea agreed last year to deploy the system to counter the threat of missile launches by North Korea. The Pentagon says the system is critical to defend South Korea and U.S. forces against North Korean missiles, and that that is its sole purpose.
But China says the system's advanced radar can penetrate deep into its territory and undermine its security, while it will do little to deter the North.
"China strongly urges the United States and South Korea to stop actions that worsen regional tensions and harm China's strategic security interests and cancel the deployment of the THAAD system and withdraw the equipment," Chinese foreign ministry spokesman Geng Shuang told a briefing.
"China will resolutely take necessary steps to defend its interests," Geng said, without elaborating.
China is North Korea's sole major ally and its support is seen as crucial to U.S.-led efforts to rein in Pyongyang.
The United States began moving the first elements of the THAAD system to South Korea in March after North Korea tested four ballistic missiles. Seoul has accused China of discriminating against South Korean companies in China because of the deployment.
Moon Jae-in, a liberal politician expected to win South Korea's election, has called for a delay in the deployment, saying the new administration should make a decision after gathering public opinion and more talks with Washington.
A spokesman for Moon said moving the parts to the site "ignored public opinion and due process" and demanded it be suspended.
Television footage showed military trailers carrying equipment, including what appeared to be launch canisters, to the battery site.
Protesters shouted and hurled water bottles at the vehicles over lines of police holding them back.
'We Will Fight'
More than 10 protesters were injured, some of them with fractures, in clashes with police, Kim Jong-kyung, a leader of villagers opposing the deployment, told Reuters.
Kim said about 200 protesters rallied overnight and they would keep up their opposition.
"There's still time for THAAD to be actually up and running so we will fight until equipment is withdrawn from the site and ask South Korea's new government to reconsider," Kim told Reuters.
A police official in the nearby town of Seongju said police had withdrawn from the area and were not aware of any injuries.
The United States and North Korea have stepped up warnings to each other in recent weeks over North Korea's development of nuclear weapons and missiles in defiance of U.N. resolutions.
North Korea's nuclear and missile threat is perhaps the most serious security challenge confronting U.S. President Donald Trump. He has vowed to prevent North Korea from being able to hit the United States with a nuclear missile.
North Korea says it needs the weapons to defend itself and has vowed to strike the United States and its Asian allies at the first sign of any attack on it.
The United States is sending the USS Carl Vinson carrier strike group to waters off the Korean peninsula, where it will join the USS Michigan, a nuclear submarine that docked in South Korea on Tuesday. South Korea's navy has said it will hold drills with the U.S. strike group.
Harris said the carrier was in the Phiippine Sea, within two-hours striking distance of North Korea "if called upon to do that".
Washington has said all options are on the table, inludeding military ones, in dealing with North Korea, but officials have stressed that the current focus is on stepped-up sanctions, which are expected to be discussed at a U.N. Security Council meeting on Friday called by U.S. Secretary of State Rex Tillerson.
North Korea's foreign ministry denounced the planned meeting, saying the United States was "not morally entitled" to force members states to impose sanctions on it.
"It is a wild dream for the U.S. to think of depriving the DPRK of its nuclear deterrent through military threat and sanctions. It is just like sweeping the sea with a broom," it said.
DPRK stands for the Democratic People's Republic of Korea, the North's official name.
China's envoy on North Korea, Wu Dawei, met his Japanese counterpart, Kenji Kanasugi, for talks in Tokyo and they agreed that they would "respond firmly" to any further North Korean provocation, Japan's foreign ministry said.
"We are against anything that might lead to war or chaos," Wu said.
KCNA said earlier leader Kim Jong Un had supervised the country's "largest-ever" live-fire drill to mark Tuesday's 85th founding anniversary of its military, with more than 300 large-calibre, self-propelled artillery pieces on its east coast.
There had been fears North Korea would mark the anniversary with its sixth nuclear test or a long-range missile launch.
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