The ministry said on Wednesday that it made the decision together with the US, adding the four launchers will be deployed with USA construction equipment and resources to augment the THAAD site in Seongju, North Gyeongsang Province.
The anti-missile defence systems are meant to protect South Korea from an attack from North Korea.
In response, U.S. President Donald Trump said "all options are on the table", not ruling out military action.
Crude oil drops in Asia despite upbeat China manufacturing PMIs
Some states, like Georgia, have seen prices rise as much as 12 cents a gallon as reduced supply has hampered distribution. It is a small release of crude for a country that uses almost 20 million barrels of petroleum products daily.
While Putin reiterated Moscow's opposition to new sanctions against North Korea, he told reporters he had assured South Korean President Moon Jae-in that Moscow condemns North Korea's nuclear test and thinks it "flagrantly violates" worldwide law.
There are now two launchers at the location, a former golf course.
The Ministry of National Defence said: "There is no change in the government's position to make the final decision on whether the THAAD system will be deployed (in South Korea) after carrying out the general environmental impact assessment of the entire site thoroughly and fairly".
'S. Korea, US Discuss Rotational Deployment of US Stealth Jets to Korea'
Tensions on the Korean Peninsula are at their highest point in years after a series of missile tests by Pyongyang. However, Trump said after the latest missile test that negotiations with Pyongyang were "not the answer".
On Aug. 30, a day after North Korea launched a ballistic missile over northern Japan, the US military joined South Korea and Japan in a spectacular show of force against the Hermit Kingdom.
"Myself and President Putin share a view that North Korea has gone the wrong way with its nuclear and missile programme and that easing tension on the Korean peninsula is an urgent issue", Mr Moon said.
However, at a news conference in China, Mr Putin stopped short of expressing support for more United Nations sanctions on North Korea, and said Russian Federation viewed them as "useless and ineffective".
Kenya on edge as Supreme Court prepares election ruling
As news of the court's decision spread, cheers and celebrations could be heard on the streets in parts of the capital, Nairobi . Three of Kenya's presidents since independence from Britain in 1963 have been Kikuyu and one has been from the Kalenjin tribe.
The leaders of South Korea and Japan are holding talks with Putin in Vladivostok on the sidelines of a conference on economic development of Russia's Far East.