Friday's move paved the way for a criminal investigation into allegations that ambassador Kim Moon-Hwan sexually assaulted several embassy employees in Addis Ababa.
"Sexual misdeeds by the head of the diplomatic mission against multiple victims have been confirmed through a thorough investigation," the ministry said in a press statement.
As well as a criminal inquiry, it said, it was seeking a "heavy punishment" from the central government disciplinary committee.
Ministry officials declined to give further details including the nationality of the victims, citing privacy concerns.
Foreign Minister Kang Kyung-wha called for strengthened oversight over diplomats working abroad, saying she was "appalled" at the scandal that undercuts the ministry's efforts to start anew with the new liberal president Moon Jae-In.
The incident is the second at the embassy in Addis Ababa.
The ministry dismissed a senior diplomat at the mission last month for raping a young female colleague after she passed out from consuming too much wine at an embassy dinner party.
That came after another South Korean diplomat stationed in Chile was found to have sexually harassed minors there in December last year. He was recalled and fired.
The move to file a complaint with prosecution authorities paved the way for a criminal investigation into allegations that ambassador Kim Moon-Hwan sexually assaulted several embassy employees in Addis Ababa.
South Korea's foreign ministry filed a complaint with prosecution authorities on Friday against its ambassador to Ethiopia for multiple sexual assaults, it said, just weeks after another diplomat at the mission was sacked for raping a female colleague.
