The Terminal High-Altitude Area Defence (THAAD) system is being deployed in South Korea to counter threats from North Korea, which on Monday test-fired another missile as it seeks to develop its nuclear weapons programme.
The left-leaning Moon, who took office this month following the ousting of impeached president Park Geun-Hye, has previously expressed ambivalence over THAAD. The system is strongly opposed by China for fear it will undermine its own military capabilities.
Moon's spokesman said the defence ministry, while briefing the de facto transition team last week, had failed to tell the new government that four more launchers had been brought into the country.
The president has not yet reshuffled the cabinet appointed by his predecessor Park Geun-Hye.
"President Moon said it was very shocking," spokesman Yoon Young-Chan told journalists.
"He ordered (an investigation) to find out how the four additional launchers were brought into the country, who made such a decision, why this has not been disclosed to the people and why this has not been reported to the new administration even to date."
One THAAD battery is usually composed of a powerful X-band radar, six mobile launchers and 48 missiles.
The conservative government under Park started installing the THAAD system to cope with North Korea's missile and nuclear threats.
But tensions between South Korea and China have risen as a result, sparking economic boycotts by Beijing. Chinese tour groups have quietly halted visits to the South and supermarkets under the Lotte brand -- the company that made land available for THAAD -- are losing business in China.
The system has also drawn strong objections from people living near the site.
Moon wants to put THAAD's deployment on hold, saying it should be discussed and approved by parliament and citing its potential impact on the country's security and environment.
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