According to the ministry, unknown gunmen attacked the Ghanaian-flagged Panofi Frontier ship at about 15:40 GMT on Wednesday, some 111 kilometres (about 69 miles) south of the Beninese coast.
Six out of 30 people, who were on board of the ship, have been kidnapped.
"It is currently unknown, who attacked the ship and where they are. On Thursday, the Foreign Ministry created a response group, based on the Overseas Korean Nationals Protection Division, and in close cooperation with the relevant bodies in South Korea and Benin will do everything possible to liberate our citizens", the statement said.
It was not immediately known whether the abductees remain unharmed, the Yonhap news agency reported. In 2014-2019, 523 South Korean citizens have been kidnapped or taken hostage, according to the Yonhap.