Moon's conservative predecessor, Park Geun-hye, had allowed the United States to deploy the Terminal High-Altitude Area Defence system to deal with North Korean nuclear threats.
A THAAD battery normally operated with six launchers, and two of them were publicly installed in a southeastern South Korean town in late April, days before Moon took office on May 10.
Last week, Moon's office said it found that four more launchers have since arrived in South Korea, but that defence officials didn't mention them in policy briefings they gave in late May. Moon demanded a probe, calling the incident "very shocking," according to his aides.
Moon's office said today that an investigation found Deputy Minister for Defence Policy Wee Seung Ho ordered ministry officials not to write clearly about the four launchers in policy reports.
More From This Section
Wee told investigators he did so because the South Korean and US militaries decided not to publicise the four launchers' arrivals, presidential official Yoon Young-chan told a televised news conference.
Yoon said Wee instead initially planned to verbally report about the four launders but didn't do so. "It's something that we cannot tolerate," Yoon said.
A THAAD battery consists of six truck-mounted launchers that can fire up to 48 interceptor missiles, fire control and communication equipment, and a powerful X-band radar officially known as AN/TPY-2.
It's unclear if Moon will go ahead with his campaign pledge to re-examine the THAAD deployment because a request for the withdrawal of the system's components could severely undermine ties with Washington, Seoul's most important ally, analysts say.
The United States stations about 28,500 troops in South Korea as deterrence against potential aggression from North Korea.