The allies had been set to sign an agreement Tuesday on setting up a joint working group to look into the roll-out of the Terminal High Altitude Area Defence System (THAAD) against North Korea's growing missile threat.
"The related accord is in the final stages but has been postponed by a day or two because of last-minute negotiations," ministry spokesman Moon Sang-Gyun said.
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The interceptor missiles carry no warheads, instead relying on kinetic energy to destroy their targets.
More than two weeks ago, the allies announced their intention to begin talks on its deployment following Pyongyang's long-range ballistic missile launch on February 7 but negotiations to launch the Joint Working Group were protracted.
The delay comes as Chinese Foreign Minister Wang Yi is set to visit Washington from Tuesday to meet his US counterpart John Kerry for possible talks over the controversial defence system and North Korea.
China opposes the proposed deployment of THAAD, with foreign ministry spokeswoman Hua Chunying warning Monday that it should not be used as a front to "undermine China's own legitimate (security) interests".
South Korea's defence ministry reiterated Tuesday that the US missile defence system only targets North Korea and that its deployment is an issue between the two allies.
The ministry said it expects official talks on THAAD to kick off next week once the two sides set up the joint working group later this week.
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