The rollout of the US-funded Terminal High-Altitude Area Defense system (Thaad) may be on hold for a year.
Four recently arrived launchers will not be deployed, an official said. Two already installed will stay in place.
Thaad aims to protect South Korea from the North's missiles, and has been criticised at home and by China.
What impact will S Korea's expanded missile defence system have?
The office of recently-elected President Moon Jae-in said that a comprehensive environmental study of Thaad was needed and that it could take up to a year to complete.
During that time, Thaad's deployment would be frozen as it was not "urgent enough" to bypass the assessment, it said.
Thaad began its rollout earlier this year under South Korea's previous presidential administration, a move which Mr Moon has said was "regrettable".
The suspension comes days after Mr Moon's office accused the defence ministry of withholding information about Thaad from the president.
It said the military did not tell Mr Moon about the delivery of the four other Thaad launchers.
The ministry has defended this decision, saying it had to uphold a confidentiality agreement with the US.
Many South Koreans have objected to Thaad, believing it will become a target and endanger the lives of those who live near its launch sites.
China has also voiced opposition to the system, saying it affects the regional security balance.
South Korea is suspending the deployment of a controversial missile defence system while the government examines its environmental impact.