"Maintaining this agreement, which was signed to facilitate the exchange of sensitive military information, does not serve our national interest," said Kim You-geun, a national security official at Seoul's presidential Blue House.
In a series of tit-for-tat measures, earlier this month Japan had removed South Korea from a so-called "white list" of countries that receive preferential export treatment.
Tokyo had done so citing security concerns and a loss of trust with South Korea, but did not provide "concrete evidence to support those allegations", said Kim.
This caused "fundamental changes" to the nature of defence cooperation, he added. The end of the General Security of Military Information Agreement (GSOMIA) marks a fresh low point in relations between the two democracies and is likely to be seen with dismay in Washington.