The Terminal High Altitude Area Defence interceptor system (THAAD) has "early capability" to respond to North Korea's nuclear and missile threat, a Defence Ministry spokesman said.
South Korean officials, however, told the Reuters news agency it would not be fully operational for some months.
The system, set up at a converted golf course in Seongju, in the country's southeast, has sparked controversy.
China sees the system as a threat, and experts have debated whether its security benefits would outweigh possible drawbacks if relations with Beijing worsen.
Some are also angry at US President Donald Trump's statement he would make Seoul pay $1bn for it.
And Seongju residents fear North Korea may target their town and are worried about the rumoured health hazards linked to system's powerful radar.
The favourite to win South Korea's presidential election on 9 May, Moon Jae-in, a liberal who calls for engagement with North Korea, has said he would reconsider THAAD if he became president.
Tensions remain high on the Korean peninsula.
Mr Trump says he is not ruling out military action against North Korea - though he has also expressed openness to a future meeting with its ruler Kim Jong-Un.
"If it would be appropriate for me to meet with him, I would absolutely, I would be honoured to do it," Mr Trump told Bloomberg News.