The system can intercept North Korean missiles although full operational capability is still some months away.
Tensions have been rising around the Korean peninsula, with repeated threats from North Korea and the presence of a group of US warships and a submarine.
North Korea reacted angrily to the latest military exercise, accusing the US of risking a nuclear war.
The rise in tension comes only a day after US President Donald Trump said he would be "honoured" to meet North Korean leader Kim Jong-un, in the right circumstances.
The US announced last week it would activate Thaad, which was not expected to be in use until late 2017, within days.
Thaad, which stands for Terminal High Altitude Area Defence, has been installed at a former golf course in the central county of Seongju, amid angry protests.
Many locals believe the system is a potential target for attacks and endangers the lives of those living nearby.
China also strongly opposes the system, believing it interferes with the security of its own military operations. On Tuesday, it demanded the deployment be halted.
Beijing would "firmly take necessary measures to uphold our interests", foreign ministry spokesman Geng Shuang said.
However, Mr Geng welcomed Mr Trump's suggestion of meeting Kim Jong-un, saying China had "always believed that dialogue and consultation... is the only realistic and viable way to achieve denuclearisation".
When the announcement of the Thaad deployment was made last year, North Korea promised a "physical response", with state media expressing the "unwavering will of our army to deal a ruthless retaliatory strike".
A spokesman for the US forces based in South Korea said Thaad now had "the ability to defend the Republic of Korea".
But the system only has "initial intercept capability", a US defence official told AFP. It will be strengthened later this year as more parts of the system arrive.
North Korea and the US have traded heated rhetoric in recent weeks as Pyongyang continues to defy a UN ban on missile tests.
North Korea has carried out two failed missile launches in recent weeks and has said it is ready to carry out its sixth nuclear test at any time.
The North reacted angrily on Tuesday to a joint US-South Korea military exercise the day before involving two supersonic B-1B Lancer bombers, which it said was a "nuclear bomb dropping drill".
"The reckless military provocation is pushing the situation on the Korean peninsula closer to the brink of nuclear war," the North's official KCNA news agency said.
What is the Terminal High Altitude Area Defense System (Thaad)?
- Shoots down short and medium-range ballistic missiles in the terminal phase of their flight
- Uses hit-to-kill technology - where kinetic energy destroys the incoming warhead
- Has a range of 200km and can reach an altitude of 150km
- US has previously deployed it in Guam and Hawaii as a measure against potential attacks from North Korea
What impact will S Korea's expanded missile defence system have?
1. The enemy launches a missile
2. The Thaad radar system detects the launch, which is relayed to command and control
3. Thaad command and control instructs the launch of an interceptor missile
4. The interceptor missile is fired at the enemy projectile
5. The enemy projectile is destroyed in the terminal phase of flight
The launcher trucks can hold up to eight interceptor missiles.
|The Thaad system only has "initial intercept capability" at present. AFP/GETTY IMAGES|
|A Terminal High Altitude Area Defense missile interceptor system is now functional at its South Korean site. In this photo from 2013, one of the THAAD systems is seen performing a test launch. Ralph Scott/U.S. Department of Defense|
THAAD missile defence system operational in South Korea
The US military's missile defence system in South Korea has reached an initial operating capability to defend against North Korean missiles, US defence officials have said.
The Terminal High Altitude Area Defence (THAAD), designed to intercept and destroy ballistic missiles during their final phase of flight, has now reached an "initial intercept capability", a US defence official, speaking on the condition of anonymity, told the AFP news agency on Monday.
Reuters, also citing anonymous US officials, confirmed the development, but cautioned that THAAD would not be fully operational for a period of months.
The US and South Korea are forging ahead with the system despite staunch objections from China.
Beijing fears THAAD will weaken its own ballistic missile capabilities and says the system upsets the regional security balance.
THAAD's deployment comes as tension soars on the Korean Peninsula following a series of missile launches by the North, and warnings from US President Donald Trump that military action is an "option on the table".
The North has carried out five nuclear tests in the past 11 years and is widely believed to be making progress on building a missile capable of delivering a warhead to the continental US.
Its foreign ministry warned on Monday that the country was prepared to carry out a nuclear test "at any time and at any location" set by its leadership.
The North will continue bolstering its "pre-emptive nuclear attack" capabilities unless Washington scraps its hostile policies, said a statement carried by the state-run KCNA news agency.
But the move has also stoked anger in South Korea. Al Jazeera's Craig Leeson, reporting from Seongju, said locals have expressed concerns over the political, economic and environmental consequences of having a THAAD in their backyard. "We're going to see protests going over the next couple days," he said.
Graham Ong-Webb, a researcher at the Institute for Defence and Strategic Studies, told Al Jazeera the THAAD will not be fully operational until late in the year, explaining that South Korea and US hope to "deter North Korea" from carrying out a missile attack.
"Some coverage is better than no coverage at this stage," he said. "I think it will improve the missile defence coverage of South korea quite significantly," adding that patriot missiles have been deployed in South Korea since 2003.
The Trump administration is meanwhile making a renewed diplomatic push to bring Pyongyang back to the negotiating table, a move China has welcomed.
Trump told the Bloomberg news agency on Monday that he would not rule out meeting North Korean leader Kim Jong-un, under the right conditions.
"If it would be appropriate for me to meet with him I would, absolutely. I would be honoured to do it," Trump said.
The White House promptly told the press that conditions were not right yet.
The US is looking for China to use its influence with Pyongyang to rein in its advancing nuclear and missile programmes, and it is unclear how Beijing will react to THAAD's activation.
China has imposed a host of measures seen as economic retaliation against the South for the THAAD deployment, including a ban on tour groups.
The system has also generated controversy in South Korea. Moon Jae-in, who is leading in polls for South Korea's May 9 presidential election, has called for deployment to be delayed until after the next administration is in place and can review the decision.
Local residents in the southern county of Seongiu, where the system is being installed on a former golf course, are worried they will be a target for North Korean missiles.
The US currently has six THAAD batteries worldwide.
THAAD Missile System In South Korea Is Now Operational, U.S. Says
An American THAAD missile defense system is now operational in South Korea, less than two months after its components arrived there, the U.S. military says.
The system is meant to protect South Korea from ballistic missiles fired by North Korea, the Pentagon says. But China and other critics of the move say it will only increase tensions on the Korean Peninsula. The decision to install the missile shield was made by the U.S. and South Korea last July.
The THAAD deployment has caused wide ripples on the peninsula, with North Korea saying the U.S. is antagonizing it and local residents protesting the installation.
Other concerns center on timing and politics.
"There's a presidential election here next week," NPR's Lauren Frayer reports from Seoul, "and the front-runner vows to renegotiate the U.S. missile defense deal. President Trump has also angered many South Koreans by saying Seoul should pay for it."
In another development, CIA Director Mike Pompeo arrived in South Korea for three days of meetings Tuesday, becoming the fourth high-level official from the Trump administration to visit (following Vice President Pence, Secretary of State Rex Tillerson and Defense Secretary James Mattis).
Pompeo began his visit by touring Yeonpyeong Island, which endured a deadly artillery and rocket attack by North Korea during a skirmish between the two countries in late 2010.
On Friday, President Trump said, "We could end up having a major, major conflict with North Korea, absolutely" — although he also said the U.S. would prefer to handle the crisis around North Korea's nuclear program by diplomatic means, and with China's help.