Hwang Kyo-Ahn and US Defence Secretary James Mattis confirmed that the two allies will go ahead with the installation of the Terminal High Altitude Area Defense (THAAD)system in the South this year as planned, the prime minister's office said.
Mattis arrived today in South Korea on the first leg of a trip that also includes Japan, two key allies rattled by US President Donald Trump's ascent to power.
It is the first overseas tour by a senior official in Trump's administration as concerns rise about the direction of American policy in the region under the protectionist and fiery leader.
The rhetoric has raised concerns in both Seoul and Tokyo, and in a statement this week South Korea's defence ministry said it hoped Mattis' trip would be "an opportunity for the Trump administration to maintain and strengthen US commitment" to their alliance.
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"President Trump ... Wanted me to make a very clear statement about the priority that we place on this alliance between our two allies", Mattis said at the start of his talks with Hwang, who serves as the South's acting leader following the impeachment of President Park Geun-Hye in December over corruption charges.
North Korean leader Kim Jong-Un boasted last month that the country was in the "final stages" of developing an intercontinental ballistic missile.
But it remains unclear whether the missile shield system would actually be deployed in South Korea after the country's leading presidential candidate and opposition member Moon Jae-In argued the decision should be left to the next government.
South Korea may hold elections in a matter of months if the Constitutional Court signs off on Park's impeachment.
The prime minister said the fact that South Korea was the first country for an overseas visit by Mattis underscored the "importance" Washington put in the alliance between the two countries.