Presidential spokesman Yoon Young-chan said Moon was "shocked” to hear that the four additional launchers of the so-called Terminal High Altitude Area Defense (THAAD) missile system were installed without being reported to the new government or to the public.
"President Moon was briefed on such facts by National Security Office (NSO) chief Chung Eui-yong and said it was very shocking,” the spokesman told a news briefing on Tuesday.
The system was initially deployed to South Korea in March with just two of its maximum load of six launchers with the declared aim of countering North Korean threats.
The South Korean official further said the president had "ordered his senior secretary for civil affairs and the NSO chief to find the truth behind the unauthorized entry of the four rocket launchers.”
The deployment of THAAD, which came amid tensions with North Korea, was met with strong opposition from people in South Korea, including the residents of Seongju County, where the missile system is installed.
The installation was agreed by the government of Moon’s predecessor Park Geun-hye, who was impeached and ousted over a corruption scandal.
During his election campaign prior to the May 9 election, Moon had urged a parliamentary review of the controversial deployment, which has angered Pyongyang, China and Russia.
Russia and China have also expressed deep concern over the controversial deployment of the American missile system on the Korean Peninsula, with Chinese officials arguing that the US system would interfere with their radars and could pose a threat to Chinese security.
Moscow also argues that the deployment would only fuel tensions in the region.