"Our government plans to deal with the THAAD deployment with a few principles while being fully aware of North Korea's nuclear and missile threats", Chung Eui-yong, the head of the presidential National Security Office, told reporters.
The deployment of the Terminal High Altitude Area Defense (THAAD) in South Korea was expected to be delayed as President Moon Jae-in ordered a legitimate environmental evaluation over the USA missile shield installation.
The South Korean Joint Chiefs of Staff said they were likely antiship missiles fired from near the city of Wonsan on North Korea's east coast that flew about 125 miles.
Chung said Seoul will continue close consultations with Washington, but added that necessary measures will be taken domestically to ensure democratic and procedural legitimacy.
South Koreans had held candlelit rallies to protest against THAAD since the deployment decision was made last July. China also says the system does nothing to deter North Korea.
Seoul's presidential office, Cheong Wa Dae, said Wednesday that deployment of four launchers for the THAAD battery should wait until the environmental study is over, though two, already-deployed launchers won't be withdrawn, a decision that the U.S. could see as a setback to its efforts to fully deploy the system as soon as possible.
President Moon on Monday ordered a probe into who tried to avoid the "green audit" of the THAAD deployment site, or a golf course at Soseong-ri village in Seongju county, North Gyeongsang province.
On Wednesday, Moon's office said the installation of four additional launchers would be halted during the environmental assessment, which may take well over a year, according to a senior administration official.
The missiles are the fourth new missile system North Korea has disclosed and tested this year, sending a defiant message that it will continue to pursue a weapons program that has rattled its neighbors and Washington.
Last month, North Korea premiered a powerful new midrange missile that outside experts said flew higher than any other missile it has tested.