Two launchers and the powerful X-band radar were already in place before his victory on May 9, but Moon expressed outrage last week when it emerged that four more launchers had been brought into the country without his knowledge.
A full THAAD battery contains six launchers mounted on trucks, each capable of firing eight interceptor missiles. But Moon's office accused an official in the Defence Ministry of deliberately failing to tell the President's staff about the arrival of the final four launchers. Moon called the omission "very shocking" and ordered an investigation. A deputy defence minister was suspended as a result.
An official from the president's office said that the missile defence system would be frozen as it is.
"We are not saying the two launchers and other equipment that has already been deployed should be withdrawn. But those that have yet to be deployed will have to wait," a senior official told reporters in Seoul, according to the Yonhap News Agency.
Gary Ross, a Pentagon spokesman, suggested that the deployment should be above politics.
"The US trusts the [South Korean] official stance that the THAAD deployment was an Alliance decision and it will not be reversed," Ross said. "We will continue to work closely with the [South Korean] Government throughout this process."
The President has ordered an environmental impact assessment of the deployment, on the grounds of a former golf course in the southern area of Seongju.
The unnamed official said the assessment could take at least a year, or perhaps two, noting that a similar evaluation for a THAAD deployment in Guam had taken 23 months, Yonhap reported.
But there was no hurry to get the system up and running, given that North Korea has been a threat to the South for years, the official said.
So far this year, North Korean leader Kim Jong Un has overseen the launch of 12 missiles, compared with the 16 that his father fired during his 17 years in power.