Thaad equipment enters Seongju site
The unannounced operation came just six days after U.S. Forces Korea (USFK) secured the land in Seongju County, North Gyeongsang, from the South Korean government.
A joint environmental survey required under the bilateral Status of Forces Agreement (SOFA) is not done yet, according to officials.
The allies signed a deal last year to deploy the Terminal High Altitude Area Defense (Thaad) system on the peninsula to help intercept North Korea's ballistic missiles.
Six trailers reportedly carrying the high-profile radar of the Thaad system and other elements were seen entering the site.
USFK issued no statement on the sensitive issue, but South Korea's Ministry of National Defense confirmed the start of the full-scale deployment.
"The measure this time is meant to secure early operational capability by positioning some available parts first at the site," the ministry said.
The two sides will proceed with the environmental assessment and construction of relevant facilities, it added.
The two sides plan to put the Thaad unit in full operation by the end of this year, according to the ministry.
Strongly protesting the move of the Thaad equipment to the site, a group of residents in the town clashed with police.